diff --git a/__fixtures__/workspace-with-lockfile-dupes/pnpm-lock.yaml b/__fixtures__/workspace-with-lockfile-dupes/pnpm-lock.yaml
index dd6cb069b9c..9345ce3e786 100644
--- a/__fixtures__/workspace-with-lockfile-dupes/pnpm-lock.yaml
+++ b/__fixtures__/workspace-with-lockfile-dupes/pnpm-lock.yaml
@@ -1,4 +1,8 @@
-lockfileVersion: '6.0'
+lockfileVersion: '6.1'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
 
 importers:
 
diff --git a/__fixtures__/workspace-with-lockfile-subdep-dupes/pnpm-lock.yaml b/__fixtures__/workspace-with-lockfile-subdep-dupes/pnpm-lock.yaml
index 3276bb9f7b6..4cdfbc30d81 100644
--- a/__fixtures__/workspace-with-lockfile-subdep-dupes/pnpm-lock.yaml
+++ b/__fixtures__/workspace-with-lockfile-subdep-dupes/pnpm-lock.yaml
@@ -1,4 +1,8 @@
-lockfileVersion: '6.0'
+lockfileVersion: '6.1'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
 
 importers:
 
diff --git a/pkg-manager/core/src/install/index.ts b/pkg-manager/core/src/install/index.ts
index 7921e2eada3..2b51ada00ba 100644
--- a/pkg-manager/core/src/install/index.ts
+++ b/pkg-manager/core/src/install/index.ts
@@ -358,6 +358,11 @@ export async function mutateModules (
       ctx.wantedLockfile.onlyBuiltDependencies = opts.onlyBuiltDependencies
       ctx.wantedLockfile.packageExtensionsChecksum = packageExtensionsChecksum
       ctx.wantedLockfile.patchedDependencies = patchedDependencies
+    } else if (!frozenLockfile) {
+      ctx.wantedLockfile.settings = {
+        autoInstallPeers: opts.autoInstallPeers,
+        excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
+      }
     }
     if (
       !ctx.lockfileHadConflicts &&
diff --git a/pkg-manager/plugin-commands-installation/test/__snapshots__/dedupe.ts.snap b/pkg-manager/plugin-commands-installation/test/__snapshots__/dedupe.ts.snap
index 45231b38e86..a7da937024e 100644
--- a/pkg-manager/plugin-commands-installation/test/__snapshots__/dedupe.ts.snap
+++ b/pkg-manager/plugin-commands-installation/test/__snapshots__/dedupe.ts.snap
@@ -15,7 +15,7 @@ exports[`pnpm dedupe updates old resolutions from importers block and removes ol
       },
 @@ -20,18 +20,6 @@
     },
-    "lockfileVersion": "6.0",
+    "lockfileVersion": "6.1",
     "packages": Object {
 -     "/ajv@6.10.2": Object {
 -       "dependencies": Object {
@@ -98,7 +98,7 @@ exports[`pnpm dedupe updates old resolutions from package block 1`] = `
 
 @@ -20,15 +20,6 @@
     },
-    "lockfileVersion": "6.0",
+    "lockfileVersion": "6.1",
     "packages": Object {
 -     "/punycode@2.1.1": Object {
 -       "dev": false,