diff --git a/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts b/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts
index b51af8e9ea3..97472b735a4 100644
--- a/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts
+++ b/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts
@@ -6,8 +6,10 @@ import { type Registries } from '@pnpm/types'
 import loadJsonFile from 'load-json-file'
 
 export interface StrictRebuildOptions {
+  autoInstallPeers: boolean
   cacheDir: string
   childConcurrency: number
+  excludeLinksFromLockfile: boolean
   extraBinPaths: string[]
   extraEnv: Record<string, string>
   lockfileDir: string
diff --git a/lockfile/lockfile-file/src/read.ts b/lockfile/lockfile-file/src/read.ts
index d07b7860b51..a4489e1757d 100644
--- a/lockfile/lockfile-file/src/read.ts
+++ b/lockfile/lockfile-file/src/read.ts
@@ -136,6 +136,8 @@ export function createLockfileObject (
   importerIds: string[],
   opts: {
     lockfileVersion: number | string
+    autoInstallPeers: boolean
+    excludeLinksFromLockfile: boolean
   }
 ) {
   const importers = importerIds.reduce((acc, importerId) => {
@@ -148,6 +150,8 @@ export function createLockfileObject (
   return {
     importers,
     lockfileVersion: opts.lockfileVersion || LOCKFILE_VERSION,
+    autoInstallPeers: opts.autoInstallPeers,
+    excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
   }
 }
 
diff --git a/lockfile/lockfile-types/src/index.ts b/lockfile/lockfile-types/src/index.ts
index acb12c072eb..cfd0135c348 100644
--- a/lockfile/lockfile-types/src/index.ts
+++ b/lockfile/lockfile-types/src/index.ts
@@ -12,6 +12,8 @@ export interface Lockfile {
   overrides?: Record<string, string>
   packageExtensionsChecksum?: string
   patchedDependencies?: Record<string, PatchFile>
+  autoInstallPeers?: boolean
+  excludeLinksFromLockfile?: boolean
 }
 
 export interface ProjectSnapshot {
@@ -33,6 +35,8 @@ export interface LockfileV6 {
   overrides?: Record<string, string>
   packageExtensionsChecksum?: string
   patchedDependencies?: Record<string, PatchFile>
+  autoInstallPeers?: boolean
+  excludeLinksFromLockfile?: boolean
 }
 
 export interface ProjectSnapshotV6 {
diff --git a/pkg-manager/core/src/getPeerDependencyIssues.ts b/pkg-manager/core/src/getPeerDependencyIssues.ts
index 963af2059a6..728b5d2c91c 100644
--- a/pkg-manager/core/src/getPeerDependencyIssues.ts
+++ b/pkg-manager/core/src/getPeerDependencyIssues.ts
@@ -20,7 +20,7 @@ export type ListMissingPeersOptions = Partial<GetContextOptions>
 | 'useGitBranchLockfile'
 | 'workspacePackages'
 >
-& Pick<GetContextOptions, 'storeDir'>
+& Pick<GetContextOptions, 'autoInstallPeers' | 'excludeLinksFromLockfile' | 'storeDir'>
 
 export async function getPeerDependencyIssues (
   projects: ProjectOptions[],
diff --git a/pkg-manager/core/src/install/index.ts b/pkg-manager/core/src/install/index.ts
index cc05fe5513e..9d4bc6eaf41 100644
--- a/pkg-manager/core/src/install/index.ts
+++ b/pkg-manager/core/src/install/index.ts
@@ -319,6 +319,8 @@ export async function mutateModules (
       : undefined
     let needsFullResolution = !maybeOpts.ignorePackageManifest &&
       lockfileIsNotUpToDate(ctx.wantedLockfile, {
+        autoInstallPeers: opts.autoInstallPeers,
+        excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
         overrides: opts.overrides,
         neverBuiltDependencies: opts.neverBuiltDependencies,
         onlyBuiltDependencies: opts.onlyBuiltDependencies,
@@ -328,7 +330,19 @@ export async function mutateModules (
       opts.fixLockfile ||
       !ctx.wantedLockfile.lockfileVersion.toString().startsWith('6.') ||
       opts.forceFullResolution
+    console.log('needsFullResolution', needsFullResolution)
+    console.log('lockf', lockfileIsNotUpToDate(ctx.wantedLockfile, {
+        autoInstallPeers: opts.autoInstallPeers,
+        excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
+        overrides: opts.overrides,
+        neverBuiltDependencies: opts.neverBuiltDependencies,
+        onlyBuiltDependencies: opts.onlyBuiltDependencies,
+        packageExtensionsChecksum,
+        patchedDependencies,
+      }))
     if (needsFullResolution) {
+      ctx.wantedLockfile.autoInstallPeers = opts.autoInstallPeers
+      ctx.wantedLockfile.excludeLinksFromLockfile = opts.excludeLinksFromLockfile
       ctx.wantedLockfile.overrides = opts.overrides
       ctx.wantedLockfile.neverBuiltDependencies = opts.neverBuiltDependencies
       ctx.wantedLockfile.onlyBuiltDependencies = opts.onlyBuiltDependencies
@@ -653,18 +667,25 @@ function lockfileIsNotUpToDate (
     overrides,
     packageExtensionsChecksum,
     patchedDependencies,
+    autoInstallPeers,
+    excludeLinksFromLockfile,
   }: {
     neverBuiltDependencies?: string[]
     onlyBuiltDependencies?: string[]
     overrides?: Record<string, string>
     packageExtensionsChecksum?: string
     patchedDependencies?: Record<string, PatchFile>
-  }) {
+    autoInstallPeers?: boolean
+    excludeLinksFromLockfile?: boolean
+  }
+) {
   return !equals(lockfile.overrides ?? {}, overrides ?? {}) ||
     !equals((lockfile.neverBuiltDependencies ?? []).sort(), (neverBuiltDependencies ?? []).sort()) ||
     !equals(onlyBuiltDependencies?.sort(), lockfile.onlyBuiltDependencies) ||
     lockfile.packageExtensionsChecksum !== packageExtensionsChecksum ||
-    !equals(lockfile.patchedDependencies ?? {}, patchedDependencies ?? {})
+    !equals(lockfile.patchedDependencies ?? {}, patchedDependencies ?? {}) ||
+    (lockfile.autoInstallPeers != null && lockfile.autoInstallPeers !== autoInstallPeers) ||
+    (lockfile.excludeLinksFromLockfile != null && lockfile.excludeLinksFromLockfile !== excludeLinksFromLockfile)
 }
 
 export function createObjectChecksum (obj: unknown) {
diff --git a/pkg-manager/core/src/link/options.ts b/pkg-manager/core/src/link/options.ts
index 49b60f9abff..6dca21a1401 100644
--- a/pkg-manager/core/src/link/options.ts
+++ b/pkg-manager/core/src/link/options.ts
@@ -9,7 +9,9 @@ import {
 import { type ReporterFunction } from '../types'
 
 interface StrictLinkOptions {
+  autoInstallPeers: boolean
   binsDir: string
+  excludeLinksFromLockfile: boolean
   force: boolean
   forceSharedLockfile: boolean
   useLockfile: boolean
diff --git a/pkg-manager/get-context/src/index.ts b/pkg-manager/get-context/src/index.ts
index dcc737cfae9..ccb75320c66 100644
--- a/pkg-manager/get-context/src/index.ts
+++ b/pkg-manager/get-context/src/index.ts
@@ -71,6 +71,8 @@ interface HookOptions {
 }
 
 export interface GetContextOptions {
+  autoInstallPeers: boolean
+  excludeLinksFromLockfile: boolean
   allProjects: Array<ProjectOptions & HookOptions>
   confirmModulesPurge?: boolean
   force: boolean
@@ -178,6 +180,8 @@ export async function getContext (
     storeDir: opts.storeDir,
     virtualStoreDir,
     ...await readLockfiles({
+      autoInstallPeers: opts.autoInstallPeers,
+      excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
       force: opts.force,
       forceSharedLockfile: opts.forceSharedLockfile,
       frozenLockfile: opts.frozenLockfile === true,
@@ -406,6 +410,8 @@ export interface PnpmSingleContext {
 export async function getContextForSingleImporter (
   manifest: ProjectManifest,
   opts: {
+    autoInstallPeers: boolean
+    excludeLinksFromLockfile: boolean
     force: boolean
     forceNewModules?: boolean
     forceSharedLockfile: boolean
@@ -520,6 +526,8 @@ export async function getContextForSingleImporter (
     storeDir,
     virtualStoreDir,
     ...await readLockfiles({
+      autoInstallPeers: opts.autoInstallPeers,
+      excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
       force: opts.force,
       forceSharedLockfile: opts.forceSharedLockfile,
       frozenLockfile: false,
diff --git a/pkg-manager/get-context/src/readLockfiles.ts b/pkg-manager/get-context/src/readLockfiles.ts
index d6ebe98de1f..d79bfdc3b62 100644
--- a/pkg-manager/get-context/src/readLockfiles.ts
+++ b/pkg-manager/get-context/src/readLockfiles.ts
@@ -26,6 +26,8 @@ export interface PnpmContext {
 
 export async function readLockfiles (
   opts: {
+    autoInstallPeers: boolean
+    excludeLinksFromLockfile: boolean
     force: boolean
     forceSharedLockfile: boolean
     frozenLockfile: boolean
@@ -103,7 +105,11 @@ export async function readLockfiles (
     })()
   )
   const files = await Promise.all<Lockfile | null | undefined>(fileReads)
-  const sopts = { lockfileVersion: wantedLockfileVersion }
+  const sopts = {
+    autoInstallPeers: opts.autoInstallPeers,
+    excludeLinksFromLockfile: opts.excludeLinksFromLockfile,
+    lockfileVersion: wantedLockfileVersion,
+  }
   const importerIds = opts.projects.map((importer) => importer.id)
   const currentLockfile = files[1] ?? createLockfileObject(importerIds, sopts)
   for (const importerId of importerIds) {
diff --git a/store/plugin-commands-store/src/storeStatus/extendStoreStatusOptions.ts b/store/plugin-commands-store/src/storeStatus/extendStoreStatusOptions.ts
index 06db4e21074..13ae869cfb5 100644
--- a/store/plugin-commands-store/src/storeStatus/extendStoreStatusOptions.ts
+++ b/store/plugin-commands-store/src/storeStatus/extendStoreStatusOptions.ts
@@ -4,6 +4,8 @@ import { type Registries } from '@pnpm/types'
 import { type ReporterFunction } from '../types'
 
 export interface StrictStoreStatusOptions {
+  autoInstallPeers: boolean
+  excludeLinksFromLockfile: boolean
   lockfileDir: string
   dir: string
   storeDir: string