diff --git a/.changeset/odd-moments-tell.md b/.changeset/odd-moments-tell.md
new file mode 100644
index 0000000000..e236cadcd1
--- /dev/null
+++ b/.changeset/odd-moments-tell.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-config": minor
+"@pnpm/workspace.manifest-writer": minor
+---
+
+`pnpm config delete --location=project` The setting in `pnpm-workspace.yaml` file will be deleted if no `.npmrc` file is present in the directory
diff --git a/config/plugin-commands-config/test/configSet.test.ts b/config/plugin-commands-config/test/configSet.test.ts
index f562d6be09..cbbcd15905 100644
--- a/config/plugin-commands-config/test/configSet.test.ts
+++ b/config/plugin-commands-config/test/configSet.test.ts
@@ -64,6 +64,34 @@ test('config set using the location=project option. The setting is written to pn
   })
 })
 
+test('config delete using the location=project option. The setting in pnpm-workspace.yaml will be deleted, when .npmrc is not present', async () => {
+  const tmp = tempDir()
+  const configDir = path.join(tmp, 'global-config')
+  fs.mkdirSync(configDir, { recursive: true })
+
+  await config.handler({
+    dir: process.cwd(),
+    cliOptions: {},
+    configDir,
+    location: 'project',
+    rawConfig: {},
+  }, ['set', 'virtual-store-dir', '.pnpm'])
+
+  expect(readYamlFile(path.join(tmp, 'pnpm-workspace.yaml'))).toEqual({
+    virtualStoreDir: '.pnpm',
+  })
+
+  await config.handler({
+    dir: process.cwd(),
+    cliOptions: {},
+    configDir,
+    location: 'project',
+    rawConfig: {},
+  }, ['delete', 'virtual-store-dir'])
+
+  expect(fs.existsSync(path.join(tmp, 'pnpm-workspace.yaml'))).toBeFalsy()
+})
+
 test('config set using the location=project option', async () => {
   const tmp = tempDir()
   const configDir = path.join(tmp, 'global-config')
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 101c89c724..b425e6fa64 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -8181,6 +8181,9 @@ importers:
       '@pnpm/workspace.read-manifest':
         specifier: workspace:*
         version: link:../read-manifest
+      ramda:
+        specifier: 'catalog:'
+        version: '@pnpm/ramda@0.28.1'
       write-yaml-file:
         specifier: 'catalog:'
         version: 5.0.0
@@ -8191,6 +8194,9 @@ importers:
       '@pnpm/workspace.manifest-writer':
         specifier: workspace:*
         version: 'link:'
+      '@types/ramda':
+        specifier: 'catalog:'
+        version: 0.29.12
       read-yaml-file:
         specifier: 'catalog:'
         version: 2.1.0
diff --git a/workspace/manifest-writer/package.json b/workspace/manifest-writer/package.json
index c82de2a52c..32b54d29bb 100644
--- a/workspace/manifest-writer/package.json
+++ b/workspace/manifest-writer/package.json
@@ -32,11 +32,13 @@
   "dependencies": {
     "@pnpm/constants": "workspace:*",
     "@pnpm/workspace.read-manifest": "workspace:*",
+    "ramda": "catalog:",
     "write-yaml-file": "catalog:"
   },
   "devDependencies": {
     "@pnpm/prepare-temp-dir": "workspace:*",
     "@pnpm/workspace.manifest-writer": "workspace:*",
+    "@types/ramda": "catalog:",
     "read-yaml-file": "catalog:"
   },
   "engines": {
diff --git a/workspace/manifest-writer/src/index.ts b/workspace/manifest-writer/src/index.ts
index 558a8b7089..77d94bf4fb 100644
--- a/workspace/manifest-writer/src/index.ts
+++ b/workspace/manifest-writer/src/index.ts
@@ -1,12 +1,30 @@
+import fs from 'fs'
 import path from 'path'
 import { readWorkspaceManifest, type WorkspaceManifest } from '@pnpm/workspace.read-manifest'
 import { WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
 import writeYamlFile from 'write-yaml-file'
+import equals from 'ramda/src/equals'
 
 export async function updateWorkspaceManifest (dir: string, updatedFields: Partial<WorkspaceManifest>): Promise<void> {
-  const manifest = await readWorkspaceManifest(dir)
-  await writeYamlFile(path.join(dir, WORKSPACE_MANIFEST_FILENAME), {
-    ...manifest,
-    ...updatedFields,
-  })
+  const manifest = await readWorkspaceManifest(dir) ?? {} as WorkspaceManifest
+  let shouldBeUpdated = false
+  for (const [key, value] of Object.entries(updatedFields)) {
+    if (!equals(manifest[key as keyof WorkspaceManifest], value)) {
+      shouldBeUpdated = true
+      if (value == null) {
+        delete manifest[key as keyof WorkspaceManifest]
+      } else {
+        // @ts-expect-error
+        manifest[key as keyof WorkspaceManifest] = value
+      }
+    }
+  }
+  if (!shouldBeUpdated) {
+    return
+  }
+  if (Object.keys(manifest).length === 0) {
+    await fs.promises.rm(path.join(dir, WORKSPACE_MANIFEST_FILENAME))
+    return
+  }
+  await writeYamlFile(path.join(dir, WORKSPACE_MANIFEST_FILENAME), manifest)
 }