diff --git a/internal/gitexec/git_test.go b/internal/gitexec/git_test.go
index 1c1672b..4553174 100644
--- a/internal/gitexec/git_test.go
+++ b/internal/gitexec/git_test.go
@@ -22,6 +22,41 @@ func TestExecRunnerCommandErrorCapturesExitCode(t *testing.T) {
 	}
 }
 
+func TestExecRunnerGitIgnoresInheritedLinkedWorktreeEnv(t *testing.T) {
+	t.Run("Should ignore inherited linked worktree env", func(t *testing.T) {
+		ctx := context.Background()
+		main := newRepo(t)
+		writeFile(t, main, "README.md", "project\n")
+		git(t, main, "add", "README.md")
+		git(t, main, "commit", "-m", "bootstrap")
+
+		linked := filepath.Join(t.TempDir(), "linked")
+		git(t, main, "worktree", "add", "-b", "feature", linked)
+
+		sidecar := newRepo(t)
+		writeFile(t, sidecar, "project/SPEC.md", "# Spec\n")
+		git(t, sidecar, "add", "project/SPEC.md")
+		git(t, sidecar, "commit", "-m", "sidecar")
+		remoteRef := "refs/remotes/origin/project/__branches__/feature"
+		want := gitOutput(t, sidecar, "rev-parse", "HEAD")
+		git(t, sidecar, "update-ref", remoteRef, want)
+
+		gitDir := gitOutput(t, linked, "rev-parse", "--absolute-git-dir")
+		t.Setenv("GIT_DIR", gitDir)
+		t.Setenv("GIT_WORK_TREE", linked)
+		t.Setenv("GIT_INDEX_FILE", filepath.Join(gitDir, "index"))
+		t.Setenv("GIT_PREFIX", "")
+
+		got, err := (&ExecRunner{}).Run(ctx, sidecar, "git", "rev-parse", remoteRef)
+		if err != nil {
+			t.Fatalf("rev-parse sidecar ref with inherited hook env: %v", err)
+		}
+		if TrimmedStdout(got) != want {
+			t.Fatalf("sidecar ref mismatch: got %q want %q", TrimmedStdout(got), want)
+		}
+	})
+}
+
 func TestGitLocalOperationsWithGoGit(t *testing.T) {
 	t.Parallel()
 
diff --git a/internal/gitexec/runner.go b/internal/gitexec/runner.go
index 4605cef..9c76f5e 100644
--- a/internal/gitexec/runner.go
+++ b/internal/gitexec/runner.go
@@ -6,7 +6,9 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"os"
 	"os/exec"
+	"path/filepath"
 	"strings"
 )
 
@@ -27,6 +29,22 @@ type ExecRunner struct{}
 
 var _ Runner = (*ExecRunner)(nil)
 
+var gitRepositoryEnv = map[string]struct{}{
+	"GIT_ALTERNATE_OBJECT_DIRECTORIES": {},
+	"GIT_COMMON_DIR":                   {},
+	"GIT_DIR":                          {},
+	"GIT_GRAFT_FILE":                   {},
+	"GIT_IMPLICIT_WORK_TREE":           {},
+	"GIT_INDEX_FILE":                   {},
+	"GIT_NAMESPACE":                    {},
+	"GIT_NO_REPLACE_OBJECTS":           {},
+	"GIT_OBJECT_DIRECTORY":             {},
+	"GIT_PREFIX":                       {},
+	"GIT_REPLACE_REF_BASE":             {},
+	"GIT_SHALLOW_FILE":                 {},
+	"GIT_WORK_TREE":                    {},
+}
+
 // Run executes name with args in dir and returns stdout and stderr.
 func (r *ExecRunner) Run(ctx context.Context, dir, name string, args ...string) (Result, error) {
 	return r.RunWithInput(ctx, dir, "", name, args...)
@@ -42,6 +60,9 @@ func (r *ExecRunner) RunWithInput(
 ) (Result, error) {
 	cmd := exec.CommandContext(ctx, name, args...)
 	cmd.Dir = dir
+	if isGitCommand(name) {
+		cmd.Env = withoutGitRepositoryEnv(os.Environ())
+	}
 	if stdin != "" {
 		cmd.Stdin = strings.NewReader(stdin)
 	}
@@ -69,6 +90,25 @@ func (r *ExecRunner) RunWithInput(
 	return result, nil
 }
 
+func isGitCommand(name string) bool {
+	base := filepath.Base(name)
+	return base == "git" || strings.EqualFold(base, "git.exe")
+}
+
+func withoutGitRepositoryEnv(env []string) []string {
+	cleaned := make([]string, 0, len(env))
+	for _, entry := range env {
+		key, _, ok := strings.Cut(entry, "=")
+		if ok {
+			if _, blocked := gitRepositoryEnv[key]; blocked {
+				continue
+			}
+		}
+		cleaned = append(cleaned, entry)
+	}
+	return cleaned
+}
+
 // CommandError wraps an external command failure with useful context.
 type CommandError struct {
 	Name   string
diff --git a/test/e2e/skeeper_lifecycle_test.go b/test/e2e/skeeper_lifecycle_test.go
index 0417252..7610c3d 100644
--- a/test/e2e/skeeper_lifecycle_test.go
+++ b/test/e2e/skeeper_lifecycle_test.go
@@ -78,6 +78,44 @@ func TestSkeeperLifecycleAcrossRealGitClones(t *testing.T) {
 	env.assertContainsFile(filepath.Join(fresh, ".git", "hooks", "pre-merge-commit"), "skeeper internal pre-commit")
 }
 
+func TestSkeeperPreCommitHookWorksInLinkedWorktree(t *testing.T) {
+	t.Run("Should sync spec changes from linked worktree pre-commit hook", func(t *testing.T) {
+		env := newE2EEnv(t)
+		project := env.newMainRepo("project")
+		env.run(project, "skeeper",
+			"init",
+			"--sidecar-name", "project-specs",
+			"--namespace", "project",
+			"--patterns", "**/SPEC.md",
+		)
+		env.writeFile(project, "README.md", "# project\n")
+		env.git(project, "add", "README.md", ".skeeper.yml", ".gitignore", ".gitattributes")
+		env.git(project, "commit", "-m", "bootstrap skeeper")
+
+		linked := filepath.Join(env.root, "linked-project")
+		env.git(project, "worktree", "add", "-b", "feature/docs", linked)
+		env.writeFile(linked, "src/auth/service.go", "package auth\n")
+		env.writeFile(linked, "src/auth/SPEC.md", "# Initial auth spec\n")
+		env.git(linked, "add", "src/auth/service.go")
+		env.git(linked, "commit", "-m", "auth: add linked worktree spec")
+		env.assertSidecarFile(
+			"project/__branches__/feature/docs",
+			"project/src/auth/SPEC.md",
+			"# Initial auth spec\n",
+		)
+
+		env.writeFile(linked, "src/auth/service.go", "package auth\n\nconst version = 2\n")
+		env.writeFile(linked, "src/auth/SPEC.md", "# Updated auth spec\n")
+		env.git(linked, "add", "src/auth/service.go")
+		env.git(linked, "commit", "-m", "auth: update linked worktree spec")
+		env.assertSidecarFile(
+			"project/__branches__/feature/docs",
+			"project/src/auth/SPEC.md",
+			"# Updated auth spec\n",
+		)
+	})
+}
+
 func TestSkeeperSharedSidecarNamespaceIsolationAcrossRepos(t *testing.T) {
 	env := newE2EEnv(t)
 	sharedRemote := env.newBareRepo("shared-specs.git")