diff --git a/.changeset/slow-panthers-refuse.md b/.changeset/slow-panthers-refuse.md
new file mode 100644
index 00000000000..7c28bf041df
--- /dev/null
+++ b/.changeset/slow-panthers-refuse.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/resolve-dependencies": patch
+"pnpm": patch
+---
+
+Don't override the root dependency when auto installing peer dependencies [#5412](https://github.com/pnpm/pnpm/issues/5412).
diff --git a/packages/core/test/install/autoInstallPeers.ts b/packages/core/test/install/autoInstallPeers.ts
index 855f71b2ff2..158655696ce 100644
--- a/packages/core/test/install/autoInstallPeers.ts
+++ b/packages/core/test/install/autoInstallPeers.ts
@@ -1,6 +1,6 @@
 import path from 'path'
 import assertProject from '@pnpm/assert-project'
-import { addDependenciesToPackage, install, mutateModules } from '@pnpm/core'
+import { addDependenciesToPackage, install, mutateModules, PackageManifest } from '@pnpm/core'
 import { prepareEmpty, preparePackages } from '@pnpm/prepare'
 import { addDistTag, REGISTRY_MOCK_PORT } from '@pnpm/registry-mock'
 import rimraf from '@zkochan/rimraf'
@@ -347,3 +347,48 @@ test('installation on a package with many complex circular dependencies does not
   prepareEmpty()
   await addDependenciesToPackage({}, ['webpack@4.46.0'], await testDefaults({ autoInstallPeers: true }))
 })
+
+test('do not override the direct dependency with an auto installed peer dependency', async () => {
+  const includedDeps = new Set([
+    '@angular-devkit/build-angular',
+    '@angular/platform-browser-dynamic',
+    'inquirer',
+    'rxjs',
+    '@angular/common',
+    'rxjs',
+  ])
+  const project = prepareEmpty()
+  await install({
+    dependencies: {
+      rxjs: '6.6.7',
+    },
+    devDependencies: {
+      'jest-preset-angular': '12.0.1',
+    },
+  }, await testDefaults({
+    autoInstallPeers: true,
+    hooks: {
+      // This hook may be removed and the test will still be valid.
+      // The only reason the hook was added to remove the packages that aren't needed for the tests and make the test faster.
+      readPackage: [
+        (pkg: PackageManifest) => {
+          for (const depType of ['dependencies', 'optionalDependencies', 'peerDependencies', 'peerDependenciesMeta']) {
+            if (pkg[depType]) {
+              for (const depName of Object.keys(pkg[depType])) {
+                if (!includedDeps.has(depName)) {
+                  delete pkg[depType][depName]
+                }
+              }
+            }
+          }
+          if (pkg.name === '@angular-devkit/build-angular' && pkg.dependencies) {
+            delete pkg.dependencies.rxjs
+          }
+          return pkg
+        },
+      ],
+    },
+  }))
+  const lockfile = await project.readLockfile()
+  expect(lockfile.dependencies.rxjs).toStrictEqual('6.6.7')
+})
diff --git a/packages/resolve-dependencies/src/resolveDependencies.ts b/packages/resolve-dependencies/src/resolveDependencies.ts
index 3b82b5719b9..96aa421d466 100644
--- a/packages/resolve-dependencies/src/resolveDependencies.ts
+++ b/packages/resolve-dependencies/src/resolveDependencies.ts
@@ -302,7 +302,7 @@ export async function resolveRootDependencies (
       })
       importerResolutionResult = {
         pkgAddresses: resolveDependenciesResult.pkgAddresses,
-        ...(await resolveDependenciesResult.resolvingPeers),
+        ...filterMissingPeers(await resolveDependenciesResult.resolvingPeers, parentPkgAliases),
       }
       pkgAddresses.push(...importerResolutionResult.pkgAddresses)
     }
@@ -680,7 +680,7 @@ async function resolveDependenciesOfDependency (
       postponedPeersResolution: resolveDependencyResult.missingPeersOfChildren != null
         ? async (parentPkgAliases) => {
           const missingPeers = await resolveDependencyResult.missingPeersOfChildren!.get()
-          return filterMissingPeers(missingPeers, {}, parentPkgAliases)
+          return filterMissingPeers({ missingPeers, resolvedPeers: {} }, parentPkgAliases)
         }
         : undefined,
     }
@@ -698,12 +698,15 @@ async function resolveDependenciesOfDependency (
     postponedResolution: async (postponedResolutionOpts) => {
       const { missingPeers, resolvedPeers } = await postponedResolution(postponedResolutionOpts)
       resolveDependencyResult.missingPeersOfChildren!.resolve(missingPeers)
-      return filterMissingPeers(missingPeers, resolvedPeers, postponedResolutionOpts.parentPkgAliases)
+      return filterMissingPeers({ missingPeers, resolvedPeers }, postponedResolutionOpts.parentPkgAliases)
     },
   }
 }
 
-function filterMissingPeers (missingPeers: MissingPeers, resolvedPeers: ResolvedPeers, parentPkgAliases: ParentPkgAliases): PeersResolutionResult {
+function filterMissingPeers (
+  { missingPeers, resolvedPeers }: PeersResolutionResult,
+  parentPkgAliases: ParentPkgAliases
+): PeersResolutionResult {
   const newMissing = {} as MissingPeers
   for (const [peerName, peerVersion] of Object.entries(missingPeers)) {
     if (parentPkgAliases[peerName]) {