diff --git a/internal/env/patch.go b/internal/env/patch.go
index 7ab5ba1..cb986ff 100644
--- a/internal/env/patch.go
+++ b/internal/env/patch.go
@@ -2,20 +2,16 @@ package env
 
 import (
 	"bufio"
+	"fmt"
 	"os"
+	"path/filepath"
 	"strings"
 
 	"github.com/joho/godotenv"
 )
 
 func Patch(path, key, value string) error {
-	existing, err := godotenv.Read(path)
-	if err != nil {
-		// If file doesn't exist, start fresh
-		existing = make(map[string]string)
-	}
-	existing[key] = value
-	return godotenv.Write(existing, path)
+	return PatchAll(path, map[string]string{key: value}, nil)
 }
 
 // ScanComments reads path and returns full-line comment lines per mode.
@@ -65,35 +61,71 @@ func ScanComments(path, mode string) ([]string, error) {
 	return collected, scanner.Err()
 }
 
-// PatchAll reads existing env from path, merges patches, writes once, then appends comments.
-// If path does not exist, starts from an empty env. comments may be nil (no-op).
+// PatchAll reads existing env from path, merges patches, and writes atomically via a
+// temp file + rename. If path does not exist, starts from an empty env.
+// comments may be nil (no-op). The original file's permissions are preserved.
 func PatchAll(path string, patches map[string]string, comments []string) error {
+	var originalMode os.FileMode = 0600
+	if fi, err := os.Stat(path); err == nil {
+		originalMode = fi.Mode().Perm()
+	} else if !os.IsNotExist(err) {
+		return err
+	}
+
 	existing, err := godotenv.Read(path)
 	if err != nil {
+		if !os.IsNotExist(err) {
+			return err
+		}
 		existing = make(map[string]string)
 	}
+
 	for k, v := range patches {
 		existing[k] = v
 	}
-	if err := godotenv.Write(existing, path); err != nil {
+
+	content, err := godotenv.Marshal(existing)
+	if err != nil {
 		return err
 	}
-	return appendComments(path, comments)
-}
 
-// appendComments appends collected comment lines to path, preceded by a blank line.
-// No-op if comments is empty.
-func appendComments(path string, comments []string) error {
-	if len(comments) == 0 {
-		return nil
+	dir := filepath.Dir(path)
+	base := filepath.Base(path)
+	tmp, err := os.CreateTemp(dir, fmt.Sprintf(".%s.*.tmp", base))
+	if err != nil {
+		return err
+	}
+	tmpName := tmp.Name()
+	committed := false
+	defer func() {
+		if !committed {
+			tmp.Close()
+			os.Remove(tmpName)
+		}
+	}()
+
+	if _, err := tmp.WriteString(content + "\n"); err != nil {
+		return err
+	}
+	if len(comments) > 0 {
+		if _, err := tmp.WriteString("\n" + strings.Join(comments, "\n") + "\n"); err != nil {
+			return err
+		}
+	}
+	if err := tmp.Sync(); err != nil {
+		return err
+	}
+	if err := tmp.Close(); err != nil {
+		return err
 	}
 
-	f, err := os.OpenFile(path, os.O_APPEND|os.O_WRONLY, 0)
-	if err != nil {
+	if err := os.Chmod(tmpName, originalMode); err != nil {
 		return err
 	}
-	defer f.Close()
 
-	_, err = f.WriteString("\n" + strings.Join(comments, "\n") + "\n")
-	return err
+	if err := os.Rename(tmpName, path); err != nil {
+		return err
+	}
+	committed = true
+	return nil
 }
diff --git a/internal/env/patch_test.go b/internal/env/patch_test.go
index 942f5a4..df9eafe 100644
--- a/internal/env/patch_test.go
+++ b/internal/env/patch_test.go
@@ -2,6 +2,7 @@ package env
 
 import (
 	"os"
+	"path/filepath"
 	"strings"
 	"testing"
 
@@ -209,3 +210,75 @@ func TestPatchAll_NonExistentFile(t *testing.T) {
 		t.Errorf("SECRET = %q, want %q", env["SECRET"], "abc123")
 	}
 }
+
+func TestPatchAll_PermissionsPreserved(t *testing.T) {
+	path := writeTempEnv(t, "KEY=old\n")
+	if err := os.Chmod(path, 0640); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := PatchAll(path, map[string]string{"KEY": "new"}, nil); err != nil {
+		t.Fatalf("PatchAll: %v", err)
+	}
+
+	fi, err := os.Stat(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if fi.Mode().Perm() != 0640 {
+		t.Errorf("mode = %04o, want 0640", fi.Mode().Perm())
+	}
+}
+
+func TestPatchAll_DefaultPermissionsForNewFile(t *testing.T) {
+	path := filepath.Join(t.TempDir(), ".env.new")
+
+	if err := PatchAll(path, map[string]string{"X": "1"}, nil); err != nil {
+		t.Fatalf("PatchAll: %v", err)
+	}
+
+	fi, err := os.Stat(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if fi.Mode().Perm() != 0600 {
+		t.Errorf("mode = %04o, want 0600", fi.Mode().Perm())
+	}
+}
+
+func TestPatchAll_TempFileRemovedOnError(t *testing.T) {
+	dir := t.TempDir()
+	// Point at a non-existent subdirectory so CreateTemp fails.
+	path := filepath.Join(dir, "nonexistent-subdir", ".env")
+
+	err := PatchAll(path, map[string]string{"KEY": "val"}, nil)
+	if err == nil {
+		t.Fatal("expected error, got nil")
+	}
+
+	entries, _ := os.ReadDir(dir)
+	for _, e := range entries {
+		if strings.HasSuffix(e.Name(), ".tmp") {
+			t.Errorf("stale temp file found: %s", e.Name())
+		}
+	}
+}
+
+func TestPatch_IsTransactional(t *testing.T) {
+	path := writeTempEnv(t, "A=1\nB=2\n")
+
+	if err := Patch(path, "A", "updated"); err != nil {
+		t.Fatalf("Patch: %v", err)
+	}
+
+	env, err := godotenv.Read(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if env["A"] != "updated" {
+		t.Errorf("A = %q, want %q", env["A"], "updated")
+	}
+	if env["B"] != "2" {
+		t.Errorf("B = %q, want %q", env["B"], "2")
+	}
+}