diff --git a/.changeset/breezy-clouds-kick.md b/.changeset/breezy-clouds-kick.md
new file mode 100644
index 0000000000..8b4dde1d16
--- /dev/null
+++ b/.changeset/breezy-clouds-kick.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-config": patch
+"pnpm": patch
+---
+
+`pnpm config set` should convert the settings to their correct type before adding them to `pnpm-workspace.yaml` [#9355](https://github.com/pnpm/pnpm/issues/9355).
diff --git a/config/plugin-commands-config/src/configSet.ts b/config/plugin-commands-config/src/configSet.ts
index b5d38fe47b..102f07c3a0 100644
--- a/config/plugin-commands-config/src/configSet.ts
+++ b/config/plugin-commands-config/src/configSet.ts
@@ -1,6 +1,7 @@
 import fs from 'fs'
 import path from 'path'
 import util from 'util'
+import { types } from '@pnpm/config'
 import { runNpm } from '@pnpm/run-npm'
 import { updateWorkspaceManifest } from '@pnpm/workspace.manifest-writer'
 import camelCase from 'camelcase'
@@ -34,10 +35,43 @@ export async function configSet (opts: ConfigCommandOptions, key: string, value:
   }
   key = camelCase(key)
   await updateWorkspaceManifest(opts.workspaceDir ?? opts.dir, {
-    [key]: value,
+    [key]: castField(value, kebabCase(key)),
   })
 }
 
+function castField (value: unknown, key: string) {
+  if (typeof value !== 'string') {
+    return value
+  }
+
+  const type = types[key as keyof typeof types] as (string | number | boolean | null | NumberConstructor)
+  const typeList = Array.isArray(type) ? type : [type]
+  const isNumber = typeList.includes(Number)
+
+  value = value.trim()
+
+  switch (value) {
+  case 'true': {
+    return true
+  }
+  case 'false': {
+    return false
+  }
+  case 'null': {
+    return null
+  }
+  case 'undefined': {
+    return undefined
+  }
+  }
+
+  if (isNumber && !isNaN(value as number)) {
+    value = Number(value)
+  }
+
+  return value
+}
+
 export function settingShouldFallBackToNpm (key: string): boolean {
   return (
     ['registry', '_auth', '_authToken', 'username', '_password'].includes(key) ||
diff --git a/config/plugin-commands-config/test/configSet.test.ts b/config/plugin-commands-config/test/configSet.test.ts
index cbbcd15905..5a27068db7 100644
--- a/config/plugin-commands-config/test/configSet.test.ts
+++ b/config/plugin-commands-config/test/configSet.test.ts
@@ -112,6 +112,24 @@ test('config set using the location=project option', async () => {
   })
 })
 
+test('config set saves the setting in the right format to pnpm-workspace.yaml', 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', 'fetch-timeout', '1000'])
+
+  expect(readYamlFile(path.join(tmp, 'pnpm-workspace.yaml'))).toEqual({
+    fetchTimeout: 1000,
+  })
+})
+
 test('config set in project .npmrc file', async () => {
   const tmp = tempDir()
   const configDir = path.join(tmp, 'global-config')