diff --git a/.changeset/easy-toys-design.md b/.changeset/easy-toys-design.md
new file mode 100644
index 0000000000..f7bff8e079
--- /dev/null
+++ b/.changeset/easy-toys-design.md
@@ -0,0 +1,10 @@
+---
+"@pnpm/plugin-commands-rebuild": major
+"@pnpm/modules-yaml": major
+"@pnpm/headless": major
+"@pnpm/build-modules": major
+"@pnpm/core": major
+"@pnpm/exec.build-commands": major
+---
+
+`ignoreBuilds` is now a set of DepPath.
diff --git a/.changeset/sharp-snakes-love.md b/.changeset/sharp-snakes-love.md
new file mode 100644
index 0000000000..b6430b948e
--- /dev/null
+++ b/.changeset/sharp-snakes-love.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/types": minor
+---
+
+Add type for IgnoredBuilds.
diff --git a/.changeset/tender-socks-show.md b/.changeset/tender-socks-show.md
new file mode 100644
index 0000000000..b846d0c568
--- /dev/null
+++ b/.changeset/tender-socks-show.md
@@ -0,0 +1,5 @@
+---
+"pnpm": patch
+---
+
+Improved reporting of ignored dependency scripts [#10276](https://github.com/pnpm/pnpm/pull/10276).
diff --git a/exec/build-commands/package.json b/exec/build-commands/package.json
index 5e1b27ba1d..141e302f06 100644
--- a/exec/build-commands/package.json
+++ b/exec/build-commands/package.json
@@ -34,6 +34,7 @@
   "dependencies": {
     "@pnpm/config": "workspace:*",
     "@pnpm/config.config-writer": "workspace:*",
+    "@pnpm/dependency-path": "workspace:*",
     "@pnpm/modules-yaml": "workspace:*",
     "@pnpm/plugin-commands-rebuild": "workspace:*",
     "@pnpm/prepare-temp-dir": "workspace:*",
diff --git a/exec/build-commands/src/getAutomaticallyIgnoredBuilds.ts b/exec/build-commands/src/getAutomaticallyIgnoredBuilds.ts
index 8467c8e6ac..bae3095e6c 100644
--- a/exec/build-commands/src/getAutomaticallyIgnoredBuilds.ts
+++ b/exec/build-commands/src/getAutomaticallyIgnoredBuilds.ts
@@ -1,4 +1,5 @@
 import path from 'path'
+import { parse } from '@pnpm/dependency-path'
 import { type Modules, readModulesManifest } from '@pnpm/modules-yaml'
 import { type IgnoredBuildsCommandOpts } from './ignoredBuilds.js'
 
@@ -11,8 +12,18 @@ export interface GetAutomaticallyIgnoredBuildsResult {
 export async function getAutomaticallyIgnoredBuilds (opts: IgnoredBuildsCommandOpts): Promise<GetAutomaticallyIgnoredBuildsResult> {
   const modulesDir = getModulesDir(opts)
   const modulesManifest = await readModulesManifest(modulesDir)
+  let automaticallyIgnoredBuilds: null | string[]
+  if (modulesManifest?.ignoredBuilds) {
+    const ignoredPkgNames = new Set<string>()
+    for (const depPath of modulesManifest?.ignoredBuilds) {
+      ignoredPkgNames.add(parse(depPath).name ?? depPath)
+    }
+    automaticallyIgnoredBuilds = Array.from(ignoredPkgNames)
+  } else {
+    automaticallyIgnoredBuilds = null
+  }
   return {
-    automaticallyIgnoredBuilds: modulesManifest && (modulesManifest.ignoredBuilds ?? []),
+    automaticallyIgnoredBuilds,
     modulesDir,
     modulesManifest,
   }
diff --git a/exec/build-commands/test/approveBuilds.test.ts b/exec/build-commands/test/approveBuilds.test.ts
index d7be81c728..3616c793c2 100644
--- a/exec/build-commands/test/approveBuilds.test.ts
+++ b/exec/build-commands/test/approveBuilds.test.ts
@@ -6,7 +6,7 @@ import { type RebuildCommandOpts } from '@pnpm/plugin-commands-rebuild'
 import { prepare } from '@pnpm/prepare'
 import { type ProjectManifest } from '@pnpm/types'
 import { getConfig } from '@pnpm/config'
-import { type Modules, readModulesManifest } from '@pnpm/modules-yaml'
+import { readModulesManifest } from '@pnpm/modules-yaml'
 import { REGISTRY_MOCK_PORT } from '@pnpm/registry-mock'
 import { jest } from '@jest/globals'
 import { loadJsonFileSync } from 'load-json-file'
@@ -124,7 +124,7 @@ test('approve no builds', async () => {
   expect(fs.readdirSync('node_modules/@pnpm.e2e/install-script-example')).not.toContain('generated-by-install.js')
 
   // Covers https://github.com/pnpm/pnpm/issues/9296
-  expect(await readModulesManifest('node_modules')).not.toHaveProperty(['ignoredBuilds' satisfies keyof Modules])
+  expect((await readModulesManifest('node_modules'))!.ignoredBuilds).toBeUndefined()
 })
 
 test("works when root project manifest doesn't exist in a workspace", async () => {
diff --git a/exec/build-commands/test/ignoredBuilds.test.ts b/exec/build-commands/test/ignoredBuilds.test.ts
index 51d23d4456..213247848f 100644
--- a/exec/build-commands/test/ignoredBuilds.test.ts
+++ b/exec/build-commands/test/ignoredBuilds.test.ts
@@ -3,6 +3,7 @@ import fs from 'fs'
 import { ignoredBuilds } from '@pnpm/exec.build-commands'
 import { tempDir } from '@pnpm/prepare-temp-dir'
 import { writeModulesManifest } from '@pnpm/modules-yaml'
+import { type DepPath } from '@pnpm/types'
 
 const DEFAULT_MODULES_MANIFEST = {
   hoistedDependencies: {},
@@ -30,7 +31,7 @@ test('ignoredBuilds lists automatically ignored dependencies', async () => {
   fs.mkdirSync(modulesDir, { recursive: true })
   await writeModulesManifest(modulesDir, {
     ...DEFAULT_MODULES_MANIFEST,
-    ignoredBuilds: ['foo'],
+    ignoredBuilds: new Set(['foo@1.0.0' as DepPath]),
   })
   const output = await ignoredBuilds.handler({
     dir,
@@ -46,7 +47,7 @@ test('ignoredBuilds lists explicitly ignored dependencies', async () => {
   fs.mkdirSync(modulesDir, { recursive: true })
   await writeModulesManifest(modulesDir, {
     ...DEFAULT_MODULES_MANIFEST,
-    ignoredBuilds: [],
+    ignoredBuilds: new Set(),
   })
   const output = await ignoredBuilds.handler({
     dir,
@@ -66,7 +67,7 @@ test('ignoredBuilds lists both automatically and explicitly ignored dependencies
   fs.mkdirSync(modulesDir, { recursive: true })
   await writeModulesManifest(modulesDir, {
     ...DEFAULT_MODULES_MANIFEST,
-    ignoredBuilds: ['foo', 'bar'],
+    ignoredBuilds: new Set(['foo@1.0.0', 'bar@1.0.0'] as DepPath[]),
   })
   const output = await ignoredBuilds.handler({
     dir,
diff --git a/exec/build-commands/tsconfig.json b/exec/build-commands/tsconfig.json
index b433bb4510..5731bbc60f 100644
--- a/exec/build-commands/tsconfig.json
+++ b/exec/build-commands/tsconfig.json
@@ -21,6 +21,9 @@
     {
       "path": "../../config/config-writer"
     },
+    {
+      "path": "../../packages/dependency-path"
+    },
     {
       "path": "../../packages/types"
     },
diff --git a/exec/build-modules/package.json b/exec/build-modules/package.json
index b4447b692d..9b0ab4bcfb 100644
--- a/exec/build-modules/package.json
+++ b/exec/build-modules/package.json
@@ -36,6 +36,7 @@
     "@pnpm/calc-dep-state": "workspace:*",
     "@pnpm/config": "workspace:*",
     "@pnpm/core-loggers": "workspace:*",
+    "@pnpm/dependency-path": "workspace:*",
     "@pnpm/deps.graph-sequencer": "workspace:*",
     "@pnpm/fs.hard-link-dir": "workspace:*",
     "@pnpm/lifecycle": "workspace:*",
diff --git a/exec/build-modules/src/index.ts b/exec/build-modules/src/index.ts
index b934ce4600..b5e2fd4d07 100644
--- a/exec/build-modules/src/index.ts
+++ b/exec/build-modules/src/index.ts
@@ -4,6 +4,7 @@ import util from 'util'
 import { calcDepState, type DepsStateCache } from '@pnpm/calc-dep-state'
 import { getWorkspaceConcurrency } from '@pnpm/config'
 import { skippedOptionalDependencyLogger } from '@pnpm/core-loggers'
+import * as dp from '@pnpm/dependency-path'
 import { runPostinstallHooks } from '@pnpm/lifecycle'
 import { linkBins, linkBinsOfPackages } from '@pnpm/link-bins'
 import { logger } from '@pnpm/logger'
@@ -11,7 +12,12 @@ import { hardLinkDir } from '@pnpm/worker'
 import { readPackageJsonFromDir, safeReadPackageJsonFromDir } from '@pnpm/read-package-json'
 import { type StoreController } from '@pnpm/store-controller-types'
 import { applyPatchToDir } from '@pnpm/patching.apply-patch'
-import { type AllowBuild, type DependencyManifest } from '@pnpm/types'
+import {
+  type AllowBuild,
+  type DependencyManifest,
+  type DepPath,
+  type IgnoredBuilds,
+} from '@pnpm/types'
 import pDefer, { type DeferredPromise } from 'p-defer'
 import { pickBy } from 'ramda'
 import runGroups from 'run-groups'
@@ -47,7 +53,7 @@ export async function buildModules<T extends string> (
     rootModulesDir: string
     hoistedLocations?: Record<string, string[]>
   }
-): Promise<{ ignoredBuilds?: string[] }> {
+): Promise<{ ignoredBuilds?: IgnoredBuilds }> {
   if (!rootDepPaths.length) return {}
   const warn = (message: string) => {
     logger.warn({ message, prefix: opts.lockfileDir })
@@ -61,7 +67,7 @@ export async function buildModules<T extends string> (
   }
   const chunks = buildSequence<T>(depGraph, rootDepPaths)
   if (!chunks.length) return {}
-  const ignoredPkgs = new Set<string>()
+  let ignoredBuilds = new Set<DepPath>()
   const allowBuild = opts.allowBuild ?? (() => true)
   const groups = chunks.map((chunk) => {
     chunk = chunk.filter((depPath) => {
@@ -77,7 +83,7 @@ export async function buildModules<T extends string> (
         let ignoreScripts = Boolean(buildDepOpts.ignoreScripts)
         if (!ignoreScripts) {
           if (depGraph[depPath].requiresBuild && !allowBuild(depGraph[depPath].name, depGraph[depPath].version)) {
-            ignoredPkgs.add(depGraph[depPath].name)
+            ignoredBuilds.add(depGraph[depPath].depPath)
             ignoreScripts = true
           }
         }
@@ -90,14 +96,15 @@ export async function buildModules<T extends string> (
   })
   await runGroups.default(getWorkspaceConcurrency(opts.childConcurrency), groups)
   if (opts.ignoredBuiltDependencies?.length) {
-    for (const ignoredBuild of opts.ignoredBuiltDependencies) {
-      // We already ignore the build of this dependency.
-      // No need to report it.
-      ignoredPkgs.delete(ignoredBuild)
-    }
+    // We already ignore the build of these dependencies.
+    // No need to report them.
+    ignoredBuilds = new Set(Array.from(ignoredBuilds).filter((ignoredPkgDepPath) =>
+      !opts.ignoredBuiltDependencies!.some((ignoredInSettings) =>
+        (ignoredInSettings === ignoredPkgDepPath) || (dp.parse(ignoredPkgDepPath).name === ignoredInSettings)
+      )
+    ))
   }
-  const packageNames = Array.from(ignoredPkgs)
-  return { ignoredBuilds: packageNames }
+  return { ignoredBuilds }
 }
 
 async function buildDependency<T extends string> (
diff --git a/exec/build-modules/tsconfig.json b/exec/build-modules/tsconfig.json
index 358e8d0e39..4e8257451c 100644
--- a/exec/build-modules/tsconfig.json
+++ b/exec/build-modules/tsconfig.json
@@ -24,6 +24,9 @@
     {
       "path": "../../packages/core-loggers"
     },
+    {
+      "path": "../../packages/dependency-path"
+    },
     {
       "path": "../../packages/logger"
     },
diff --git a/exec/plugin-commands-rebuild/src/implementation/index.ts b/exec/plugin-commands-rebuild/src/implementation/index.ts
index 053f3ddbd0..ffbbf16266 100644
--- a/exec/plugin-commands-rebuild/src/implementation/index.ts
+++ b/exec/plugin-commands-rebuild/src/implementation/index.ts
@@ -26,7 +26,13 @@ import { lockfileWalker, type LockfileWalkerStep } from '@pnpm/lockfile.walker'
 import { logger, streamParser } from '@pnpm/logger'
 import { writeModulesManifest } from '@pnpm/modules-yaml'
 import { createOrConnectStoreController } from '@pnpm/store-connection-manager'
-import { type DepPath, type ProjectManifest, type ProjectId, type ProjectRootDir } from '@pnpm/types'
+import {
+  type DepPath,
+  type IgnoredBuilds,
+  type ProjectManifest,
+  type ProjectId,
+  type ProjectRootDir,
+} from '@pnpm/types'
 import { createAllowBuildFunction } from '@pnpm/builder.policy'
 import { pkgRequiresBuild } from '@pnpm/exec.pkg-requires-build'
 import * as dp from '@pnpm/dependency-path'
@@ -92,7 +98,7 @@ export async function rebuildSelectedPkgs (
   projects: Array<{ buildIndex: number, manifest: ProjectManifest, rootDir: ProjectRootDir }>,
   pkgSpecs: string[],
   maybeOpts: RebuildOptions
-): Promise<{ ignoredBuilds?: string[] }> {
+): Promise<{ ignoredBuilds?: IgnoredBuilds }> {
   const reporter = maybeOpts?.reporter
   if ((reporter != null) && typeof reporter === 'function') {
     streamParser.on('data', reporter)
@@ -269,7 +275,7 @@ async function _rebuild (
     extraNodePaths: string[]
   } & Pick<PnpmContext, 'modulesFile'>,
   opts: StrictRebuildOptions
-): Promise<{ pkgsThatWereRebuilt: Set<string>, ignoredPkgs: string[] }> {
+): Promise<{ pkgsThatWereRebuilt: Set<string>, ignoredPkgs: IgnoredBuilds }> {
   const depGraph = lockfileToDepGraph(ctx.currentLockfile)
   const depsStateCache: DepsStateCache = {}
   const pkgsThatWereRebuilt = new Set<string>()
@@ -309,12 +315,12 @@ async function _rebuild (
     logger.info({ message, prefix: opts.dir })
   }
 
-  const ignoredPkgs: string[] = []
+  const ignoredPkgs = new Set<DepPath>()
   const _allowBuild = createAllowBuildFunction(opts) ?? (() => true)
-  const allowBuild = (pkgName: string, version: string) => {
+  const allowBuild = (pkgName: string, version: string, depPath: DepPath) => {
     if (_allowBuild(pkgName, version)) return true
     if (!opts.ignoredBuiltDependencies?.includes(pkgName)) {
-      ignoredPkgs.push(pkgName)
+      ignoredPkgs.add(depPath)
     }
     return false
   }
@@ -370,7 +376,7 @@ async function _rebuild (
           requiresBuild = pkgRequiresBuild(pgkManifest, {})
         }
 
-        const hasSideEffects = requiresBuild && allowBuild(pkgInfo.name, pkgInfo.version) && await runPostinstallHooks({
+        const hasSideEffects = requiresBuild && allowBuild(pkgInfo.name, pkgInfo.version, depPath) && await runPostinstallHooks({
           depPath,
           extraBinPaths,
           extraEnv: opts.extraEnv,
diff --git a/packages/dependency-path/test/index.ts b/packages/dependency-path/test/index.ts
index e05259ab0b..be01897deb 100644
--- a/packages/dependency-path/test/index.ts
+++ b/packages/dependency-path/test/index.ts
@@ -7,6 +7,7 @@ import {
   refToRelative,
   tryGetPackageId,
   isRuntimeDepPath,
+  removeSuffix,
 } from '@pnpm/dependency-path'
 import { type DepPath } from '@pnpm/types'
 
@@ -145,3 +146,7 @@ test('isRuntimeDepPath', () => {
   expect(isRuntimeDepPath('node@runtime:20.1.0' as DepPath)).toBeTruthy()
   expect(isRuntimeDepPath('node@20.1.0' as DepPath)).toBeFalsy()
 })
+
+test('removeSuffix', () => {
+  expect(removeSuffix('foo@1.0.0(patch_hash=0000)(@types/babel__core@7.1.14)')).toBe('foo@1.0.0')
+})
diff --git a/packages/types/src/misc.ts b/packages/types/src/misc.ts
index 6a4787453b..2dc059cd84 100644
--- a/packages/types/src/misc.ts
+++ b/packages/types/src/misc.ts
@@ -42,3 +42,5 @@ export type PinnedVersion =
   | 'patch'
   | 'minor'
   | 'major'
+
+export type IgnoredBuilds = Set<DepPath>
diff --git a/pkg-manager/core/package.json b/pkg-manager/core/package.json
index 30f0f37e84..8b7b2dc5a3 100644
--- a/pkg-manager/core/package.json
+++ b/pkg-manager/core/package.json
@@ -106,6 +106,7 @@
     "@pnpm/store-controller-types": "workspace:*",
     "@pnpm/symlink-dependency": "workspace:*",
     "@pnpm/types": "workspace:*",
+    "@pnpm/util.lex-comparator": "catalog:",
     "@zkochan/rimraf": "catalog:",
     "enquirer": "catalog:",
     "is-inner-link": "catalog:",
diff --git a/pkg-manager/core/src/install/index.ts b/pkg-manager/core/src/install/index.ts
index d7a8e593d21..bc77ae56e0 100644
--- a/pkg-manager/core/src/install/index.ts
+++ b/pkg-manager/core/src/install/index.ts
@@ -17,6 +17,7 @@ import {
   summaryLogger,
 } from '@pnpm/core-loggers'
 import { hashObjectNullableWithPrefix } from '@pnpm/crypto.object-hasher'
+import * as dp from '@pnpm/dependency-path'
 import {
   calcPatchHashes,
   createOverridesMapFromParsed,
@@ -67,12 +68,14 @@ import {
   type DepPath,
   type DependenciesField,
   type DependencyManifest,
+  type IgnoredBuilds,
   type PeerDependencyIssues,
   type ProjectId,
   type ProjectManifest,
   type ReadPackageHook,
   type ProjectRootDir,
 } from '@pnpm/types'
+import { lexCompare } from '@pnpm/util.lex-comparator'
 import isSubdir from 'is-subdir'
 import pLimit from 'p-limit'
 import { map as mapValues, clone, isEmpty, pipeWith, props } from 'ramda'
@@ -151,7 +154,7 @@ export interface InstallResult {
    */
   updatedCatalogs: Catalogs | undefined
   updatedManifest: ProjectManifest
-  ignoredBuilds: string[] | undefined
+  ignoredBuilds: IgnoredBuilds | undefined
 }
 
 export async function install (
@@ -204,7 +207,7 @@ export type MutateModulesOptions = InstallOptions & {
 export interface MutateModulesInSingleProjectResult {
   updatedCatalogs: Catalogs | undefined
   updatedProject: UpdatedProject
-  ignoredBuilds: string[] | undefined
+  ignoredBuilds: IgnoredBuilds | undefined
 }
 
 export async function mutateModulesInSingleProject (
@@ -246,7 +249,7 @@ export interface MutateModulesResult {
   updatedProjects: UpdatedProject[]
   stats: InstallationResultStats
   depsRequiringBuild?: DepPath[]
-  ignoredBuilds: string[] | undefined
+  ignoredBuilds: IgnoredBuilds | undefined
 }
 
 const pickCatalogSpecifier: CatalogResultMatcher<string | undefined> = {
@@ -365,10 +368,14 @@ export async function mutateModules (
   }
 
   let ignoredBuilds = result.ignoredBuilds
-  if (!opts.ignoreScripts && ignoredBuilds?.length) {
+  if (!opts.ignoreScripts && ignoredBuilds?.size) {
     ignoredBuilds = await runUnignoredDependencyBuilds(opts, ignoredBuilds)
   }
-  ignoredScriptsLogger.debug({ packageNames: ignoredBuilds })
+  if (!opts.neverBuiltDependencies) {
+    ignoredScriptsLogger.debug({
+      packageNames: ignoredBuilds ? dedupePackageNamesFromIgnoredBuilds(ignoredBuilds) : [],
+    })
+  }
 
   if ((reporter != null) && typeof reporter === 'function') {
     streamParser.removeListener('data', reporter)
@@ -387,7 +394,7 @@ export async function mutateModules (
     readonly updatedProjects: UpdatedProject[]
     readonly stats?: InstallationResultStats
     readonly depsRequiringBuild?: DepPath[]
-    readonly ignoredBuilds: string[] | undefined
+    readonly ignoredBuilds: IgnoredBuilds | undefined
   }
 
   async function _install (): Promise<InnerInstallResult> {
@@ -878,17 +885,19 @@ Note that in CI environments, this setting is enabled by default.`,
   }
 }
 
-async function runUnignoredDependencyBuilds (opts: StrictInstallOptions, previousIgnoredBuilds: string[]): Promise<string[]> {
+async function runUnignoredDependencyBuilds (opts: StrictInstallOptions, previousIgnoredBuilds: IgnoredBuilds): Promise<Set<DepPath>> {
   if (!opts.onlyBuiltDependencies?.length) {
     return previousIgnoredBuilds
   }
   const onlyBuiltDeps = createPackageVersionPolicy(opts.onlyBuiltDependencies)
-  const pkgsToBuild = previousIgnoredBuilds.flatMap((ignoredPkg) => {
-    const matchResult = onlyBuiltDeps(ignoredPkg)
+  const pkgsToBuild = Array.from(previousIgnoredBuilds).flatMap((ignoredPkg) => {
+    const ignoredPkgName = dp.parse(ignoredPkg).name
+    if (!ignoredPkgName) return []
+    const matchResult = onlyBuiltDeps(ignoredPkgName)
     if (matchResult === true) {
-      return [ignoredPkg]
+      return [ignoredPkgName]
     } else if (Array.isArray(matchResult)) {
-      return matchResult.map(version => `${ignoredPkg}@${version}`)
+      return matchResult.map(version => `${ignoredPkgName}@${version}`)
     }
     return []
   })
@@ -1068,7 +1077,7 @@ interface InstallFunctionResult {
   projects: UpdatedProject[]
   stats?: InstallationResultStats
   depsRequiringBuild: DepPath[]
-  ignoredBuilds?: string[]
+  ignoredBuilds?: IgnoredBuilds
 }
 
 type InstallFunction = (
@@ -1288,7 +1297,7 @@ const _installInContext: InstallFunction = async (projects, ctx, opts) => {
   }
   let stats: InstallationResultStats | undefined
   const allowBuild = createAllowBuildFunction(opts)
-  let ignoredBuilds: string[] | undefined
+  let ignoredBuilds: IgnoredBuilds | undefined
   if (!opts.lockfileOnly && !isInstallationOnlyForLockfileCheck && opts.enableModulesDir) {
     const result = await linkPackages(
       projects,
@@ -1388,8 +1397,13 @@ const _installInContext: InstallFunction = async (projects, ctx, opts) => {
           unsafePerm: opts.unsafePerm,
           userAgent: opts.userAgent,
         })).ignoredBuilds
-        if (ignoredBuilds == null && ctx.modulesFile?.ignoredBuilds?.length) {
-          ignoredBuilds = ctx.modulesFile.ignoredBuilds
+        if (ctx.modulesFile?.ignoredBuilds?.size) {
+          ignoredBuilds ??= new Set()
+          for (const ignoredBuild of ctx.modulesFile.ignoredBuilds.values()) {
+            if (result.currentLockfile.packages?.[ignoredBuild]) {
+              ignoredBuilds.add(ignoredBuild)
+            }
+          }
         }
       }
     }
@@ -1720,3 +1734,16 @@ async function linkAllBins (
     depNodes.map(async depNode => limitLinking(async () => linkBinsOfDependencies(depNode, depGraph, opts)))
   )
 }
+
+export class IgnoredBuildsError extends PnpmError {
+  constructor (ignoredBuilds: IgnoredBuilds) {
+    const packageNames = dedupePackageNamesFromIgnoredBuilds(ignoredBuilds)
+    super('IGNORED_BUILDS', `Ignored build scripts: ${packageNames.join(', ')}`, {
+      hint: 'Run "pnpm approve-builds" to pick which dependencies should be allowed to run scripts.',
+    })
+  }
+}
+
+function dedupePackageNamesFromIgnoredBuilds (ignoredBuilds: IgnoredBuilds): string[] {
+  return Array.from(new Set(Array.from(ignoredBuilds ?? []).map(dp.removeSuffix))).sort(lexCompare)
+}
diff --git a/pkg-manager/core/test/install/lifecycleScripts.ts b/pkg-manager/core/test/install/lifecycleScripts.ts
index 46aa338a2c..8fcd6db1af 100644
--- a/pkg-manager/core/test/install/lifecycleScripts.ts
+++ b/pkg-manager/core/test/install/lifecycleScripts.ts
@@ -486,7 +486,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependencies',
 
   {
     const ignoredPkgsLog = reporter.getCalls().find((call) => call.firstArg.name === 'pnpm:ignored-scripts')?.firstArg
-    expect(ignoredPkgsLog.packageNames).toStrictEqual(['@pnpm.e2e/pre-and-postinstall-scripts-example'])
+    expect(ignoredPkgsLog.packageNames).toStrictEqual(['@pnpm.e2e/pre-and-postinstall-scripts-example@1.0.0'])
   }
   reporter.resetHistory()
 
@@ -527,7 +527,7 @@ test('selectively allow scripts in some dependencies by onlyBuiltDependencies us
 
   {
     const ignoredPkgsLog = reporter.getCalls().find((call) => call.firstArg.name === 'pnpm:ignored-scripts')?.firstArg
-    expect(ignoredPkgsLog.packageNames).toStrictEqual(['@pnpm.e2e/pre-and-postinstall-scripts-example'])
+    expect(ignoredPkgsLog.packageNames).toStrictEqual(['@pnpm.e2e/pre-and-postinstall-scripts-example@1.0.0'])
   }
   reporter.resetHistory()
 
diff --git a/pkg-manager/headless/src/index.ts b/pkg-manager/headless/src/index.ts
index 066c67f9fa..2a59a8dd44 100644
--- a/pkg-manager/headless/src/index.ts
+++ b/pkg-manager/headless/src/index.ts
@@ -62,6 +62,7 @@ import {
   type DepPath,
   type DependencyManifest,
   type HoistedDependencies,
+  type IgnoredBuilds,
   type ProjectId,
   type ProjectManifest,
   type Registries,
@@ -186,7 +187,7 @@ export interface InstallationResultStats {
 
 export interface InstallationResult {
   stats: InstallationResultStats
-  ignoredBuilds: string[] | undefined
+  ignoredBuilds: IgnoredBuilds | undefined
 }
 
 export async function headlessInstall (opts: HeadlessOptions): Promise<InstallationResult> {
@@ -512,7 +513,7 @@ export async function headlessInstall (opts: HeadlessOptions): Promise<Installat
           .map(({ depPath }) => depPath)
       )
   }
-  let ignoredBuilds: string[] | undefined
+  let ignoredBuilds: IgnoredBuilds | undefined
   if ((!opts.ignoreScripts || Object.keys(opts.patchedDependencies ?? {}).length > 0) && opts.enableModulesDir !== false) {
     const directNodes = new Set<string>()
     for (const id of union(importerIds, ['.'])) {
@@ -557,8 +558,13 @@ export async function headlessInstall (opts: HeadlessOptions): Promise<Installat
       unsafePerm: opts.unsafePerm,
       userAgent: opts.userAgent,
     })).ignoredBuilds
-    if (ignoredBuilds == null && opts.modulesFile?.ignoredBuilds?.length) {
-      ignoredBuilds = opts.modulesFile.ignoredBuilds
+    if (opts.modulesFile?.ignoredBuilds?.size) {
+      ignoredBuilds ??= new Set()
+      for (const ignoredBuild of opts.modulesFile.ignoredBuilds.values()) {
+        if (filteredLockfile.packages?.[ignoredBuild]) {
+          ignoredBuilds.add(ignoredBuild)
+        }
+      }
     }
   }
 
diff --git a/pkg-manager/modules-yaml/src/index.ts b/pkg-manager/modules-yaml/src/index.ts
index 5637190046..5b0f65fe96 100644
--- a/pkg-manager/modules-yaml/src/index.ts
+++ b/pkg-manager/modules-yaml/src/index.ts
@@ -1,5 +1,11 @@
 import path from 'path'
-import { type DepPath, type DependenciesField, type HoistedDependencies, type Registries } from '@pnpm/types'
+import {
+  type DepPath,
+  type DependenciesField,
+  type HoistedDependencies,
+  type IgnoredBuilds,
+  type Registries,
+} from '@pnpm/types'
 import readYamlFile from 'read-yaml-file'
 import { map as mapValues } from 'ramda'
 import isWindows from 'is-windows'
@@ -13,7 +19,7 @@ export type IncludedDependencies = {
   [dependenciesField in DependenciesField]: boolean
 }
 
-export interface Modules {
+interface ModulesRaw {
   hoistedAliases?: { [depPath: DepPath]: string[] } // for backward compatibility
   hoistedDependencies: HoistedDependencies
   hoistPattern?: string[]
@@ -22,7 +28,7 @@ export interface Modules {
   nodeLinker?: 'hoisted' | 'isolated' | 'pnp'
   packageManager: string
   pendingBuilds: string[]
-  ignoredBuilds?: string[]
+  ignoredBuilds?: DepPath[]
   prunedAt: string
   registries?: Registries // nullable for backward compatibility
   shamefullyHoist?: boolean // for backward compatibility
@@ -35,18 +41,26 @@ export interface Modules {
   hoistedLocations?: Record<string, string[]>
 }
 
+export type Modules = Omit<ModulesRaw, 'ignoredBuilds'> & {
+  ignoredBuilds?: IgnoredBuilds
+}
+
 export async function readModulesManifest (modulesDir: string): Promise<Modules | null> {
   const modulesYamlPath = path.join(modulesDir, MODULES_FILENAME)
-  let modules!: Modules
+  let modulesRaw!: ModulesRaw
   try {
-    modules = await readYamlFile.default<Modules>(modulesYamlPath)
-    if (!modules) return modules
+    modulesRaw = await readYamlFile.default<ModulesRaw>(modulesYamlPath)
+    if (!modulesRaw) return modulesRaw
   } catch (err: any) { // eslint-disable-line
     if ((err as NodeJS.ErrnoException).code !== 'ENOENT') {
       throw err
     }
     return null
   }
+  const modules = {
+    ...modulesRaw,
+    ignoredBuilds: modulesRaw.ignoredBuilds ? new Set<DepPath>(modulesRaw.ignoredBuilds) : undefined,
+  }
   if (!modules.virtualStoreDir) {
     modules.virtualStoreDir = path.join(modulesDir, '.pnpm')
   } else if (!path.isAbsolute(modules.virtualStoreDir)) {
@@ -107,7 +121,7 @@ export async function writeModulesManifest (
   }
 ): Promise<void> {
   const modulesYamlPath = path.join(modulesDir, MODULES_FILENAME)
-  const saveModules = { ...modules }
+  const saveModules = { ...modules, ignoredBuilds: modules.ignoredBuilds ? Array.from(modules.ignoredBuilds) : undefined }
   if (saveModules.skipped) saveModules.skipped.sort()
 
   if (saveModules.hoistPattern == null || (saveModules.hoistPattern as unknown) === '') {
diff --git a/pkg-manager/modules-yaml/test/index.ts b/pkg-manager/modules-yaml/test/index.ts
index e84462235e..b0433c0fec 100644
--- a/pkg-manager/modules-yaml/test/index.ts
+++ b/pkg-manager/modules-yaml/test/index.ts
@@ -1,21 +1,21 @@
 /// <reference path="../../../__typings__/index.d.ts"/>
 import fs from 'fs'
 import path from 'path'
-import { readModulesManifest, writeModulesManifest } from '@pnpm/modules-yaml'
+import { readModulesManifest, writeModulesManifest, type StrictModules } from '@pnpm/modules-yaml'
 import { sync as readYamlFile } from 'read-yaml-file'
 import isWindows from 'is-windows'
 import { temporaryDirectory } from 'tempy'
 
 test('writeModulesManifest() and readModulesManifest()', async () => {
   const modulesDir = temporaryDirectory()
-  const modulesYaml = {
+  const modulesYaml: StrictModules = {
     hoistedDependencies: {},
     included: {
       dependencies: true,
       devDependencies: true,
       optionalDependencies: true,
     },
-    ignoredBuilds: [],
+    ignoredBuilds: new Set(),
     layoutVersion: 1,
     packageManager: 'pnpm@2',
     pendingBuilds: [],
@@ -66,14 +66,14 @@ test('backward compatible read of .modules.yaml created with shamefully-hoist=fa
 
 test('readModulesManifest() should not create a node_modules directory if it does not exist', async () => {
   const modulesDir = path.join(temporaryDirectory(), 'node_modules')
-  const modulesYaml = {
+  const modulesYaml: StrictModules = {
     hoistedDependencies: {},
     included: {
       dependencies: true,
       devDependencies: true,
       optionalDependencies: true,
     },
-    ignoredBuilds: [],
+    ignoredBuilds: new Set(),
     layoutVersion: 1,
     packageManager: 'pnpm@2',
     pendingBuilds: [],
@@ -94,14 +94,14 @@ test('readModulesManifest() should not create a node_modules directory if it doe
 
 test('readModulesManifest() should create a node_modules directory if makeModuleDir is set to true', async () => {
   const modulesDir = path.join(temporaryDirectory(), 'node_modules')
-  const modulesYaml = {
+  const modulesYaml: StrictModules = {
     hoistedDependencies: {},
     included: {
       dependencies: true,
       devDependencies: true,
       optionalDependencies: true,
     },
-    ignoredBuilds: [],
+    ignoredBuilds: new Set(),
     layoutVersion: 1,
     packageManager: 'pnpm@2',
     pendingBuilds: [],
diff --git a/pkg-manager/plugin-commands-installation/src/errors.ts b/pkg-manager/plugin-commands-installation/src/errors.ts
deleted file mode 100644
index 14905da32b..0000000000
--- a/pkg-manager/plugin-commands-installation/src/errors.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-import { PnpmError } from '@pnpm/error'
-
-export class IgnoredBuildsError extends PnpmError {
-  constructor (ignoredBuilds: string[]) {
-    super('IGNORED_BUILDS', `Ignored build scripts: ${ignoredBuilds.join(', ')}`, {
-      hint: 'Run "pnpm approve-builds" to pick which dependencies should be allowed to run scripts.',
-    })
-  }
-}
diff --git a/pkg-manager/plugin-commands-installation/src/installDeps.ts b/pkg-manager/plugin-commands-installation/src/installDeps.ts
index 9dc7c40bd3..70a5782f9b 100644
--- a/pkg-manager/plugin-commands-installation/src/installDeps.ts
+++ b/pkg-manager/plugin-commands-installation/src/installDeps.ts
@@ -15,6 +15,7 @@ import { rebuildProjects } from '@pnpm/plugin-commands-rebuild'
 import { createOrConnectStoreController, type CreateStoreControllerOptions } from '@pnpm/store-connection-manager'
 import { type IncludedDependencies, type Project, type ProjectsGraph, type ProjectRootDir, type PrepareExecutionEnv } from '@pnpm/types'
 import {
+  IgnoredBuildsError,
   install,
   mutateModulesInSingleProject,
   type MutateModulesOptions,
@@ -26,7 +27,6 @@ import { updateWorkspaceManifest } from '@pnpm/workspace.manifest-writer'
 import { createPkgGraph } from '@pnpm/workspace.pkgs-graph'
 import { updateWorkspaceState, type WorkspaceStateSettings } from '@pnpm/workspace.state'
 import isSubdir from 'is-subdir'
-import { IgnoredBuildsError } from './errors.js'
 import { getPinnedVersion } from './getPinnedVersion.js'
 import { getSaveType } from './getSaveType.js'
 import { getNodeExecPath } from './nodeExecPath.js'
@@ -343,7 +343,7 @@ when running add/update with the --workspace option')
         configDependencies: opts.configDependencies,
       })
     }
-    if (opts.strictDepBuilds && ignoredBuilds?.length) {
+    if (opts.strictDepBuilds && ignoredBuilds?.size) {
       throw new IgnoredBuildsError(ignoredBuilds)
     }
     return
@@ -364,7 +364,7 @@ when running add/update with the --workspace option')
       }),
     ])
   }
-  if (opts.strictDepBuilds && ignoredBuilds?.length) {
+  if (opts.strictDepBuilds && ignoredBuilds?.size) {
     throw new IgnoredBuildsError(ignoredBuilds)
   }
 
diff --git a/pkg-manager/plugin-commands-installation/src/recursive.ts b/pkg-manager/plugin-commands-installation/src/recursive.ts
index 71738d7c1e..f16fd4d6c7 100755
--- a/pkg-manager/plugin-commands-installation/src/recursive.ts
+++ b/pkg-manager/plugin-commands-installation/src/recursive.ts
@@ -23,6 +23,7 @@ import { requireHooks } from '@pnpm/pnpmfile'
 import { sortPackages } from '@pnpm/sort-packages'
 import { createOrConnectStoreController, type CreateStoreControllerOptions } from '@pnpm/store-connection-manager'
 import {
+  type IgnoredBuilds,
   type IncludedDependencies,
   type PackageManifest,
   type Project,
@@ -34,6 +35,7 @@ import {
 import { updateWorkspaceManifest } from '@pnpm/workspace.manifest-writer'
 import {
   addDependenciesToPackage,
+  IgnoredBuildsError,
   install,
   type InstallOptions,
   type MutatedProject,
@@ -50,7 +52,6 @@ import { createWorkspaceSpecs, updateToWorkspacePackagesFromManifest } from './u
 import { getSaveType } from './getSaveType.js'
 import { getPinnedVersion } from './getPinnedVersion.js'
 import { type PreferredVersions } from '@pnpm/resolver-base'
-import { IgnoredBuildsError } from './errors.js'
 
 export type RecursiveOptions = CreateStoreControllerOptions & Pick<Config,
 | 'bail'
@@ -299,7 +300,7 @@ export async function recursive (
       }))
       await Promise.all(promises)
     }
-    if (opts.strictDepBuilds && ignoredBuilds?.length) {
+    if (opts.strictDepBuilds && ignoredBuilds?.size) {
       throw new IgnoredBuildsError(ignoredBuilds)
     }
     return true
@@ -355,7 +356,7 @@ export async function recursive (
         interface ActionResult {
           updatedCatalogs?: Catalogs
           updatedManifest: ProjectManifest
-          ignoredBuilds: string[] | undefined
+          ignoredBuilds: IgnoredBuilds | undefined
         }
 
         type ActionFunction = (manifest: PackageManifest | ProjectManifest, opts: ActionOpts) => Promise<ActionResult>
@@ -419,7 +420,7 @@ export async function recursive (
             Object.assign(updatedCatalogs, newCatalogsAddition)
           }
         }
-        if (opts.strictDepBuilds && ignoredBuilds?.length) {
+        if (opts.strictDepBuilds && ignoredBuilds?.size) {
           throw new IgnoredBuildsError(ignoredBuilds)
         }
         result[rootDir].status = 'passed'
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 6e65d93b5a..57deee9ab1 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -2508,6 +2508,9 @@ importers:
       '@pnpm/config.config-writer':
         specifier: workspace:*
         version: link:../../config/config-writer
+      '@pnpm/dependency-path':
+        specifier: workspace:*
+        version: link:../../packages/dependency-path
       '@pnpm/logger':
         specifier: 'catalog:'
         version: 1001.0.0
@@ -2581,6 +2584,9 @@ importers:
       '@pnpm/core-loggers':
         specifier: workspace:*
         version: link:../../packages/core-loggers
+      '@pnpm/dependency-path':
+        specifier: workspace:*
+        version: link:../../packages/dependency-path
       '@pnpm/deps.graph-sequencer':
         specifier: workspace:*
         version: link:../../deps/graph-sequencer
@@ -5087,6 +5093,9 @@ importers:
       '@pnpm/types':
         specifier: workspace:*
         version: link:../../packages/types
+      '@pnpm/util.lex-comparator':
+        specifier: 'catalog:'
+        version: 3.0.2
       '@pnpm/worker':
         specifier: workspace:^
         version: link:../../worker
diff --git a/pnpm/test/install/lifecycleScripts.ts b/pnpm/test/install/lifecycleScripts.ts
index ead18d2d2b..5dc4a1b9b4 100644
--- a/pnpm/test/install/lifecycleScripts.ts
+++ b/pnpm/test/install/lifecycleScripts.ts
@@ -383,8 +383,8 @@ test('the list of ignored builds is preserved after a repeat install', async ()
   expect(result.stdout.toString()).toContain('Ignored build scripts:')
 
   const modulesManifest = project.readModulesManifest()
-  expect(modulesManifest?.ignoredBuilds?.sort()).toStrictEqual([
-    '@pnpm.e2e/pre-and-postinstall-scripts-example',
-    'esbuild',
+  expect(Array.from(modulesManifest!.ignoredBuilds!).sort()).toStrictEqual([
+    '@pnpm.e2e/pre-and-postinstall-scripts-example@1.0.0',
+    'esbuild@0.25.0',
   ])
 })