diff --git a/README.md b/README.md
index ea24f6b..ab6f494 100644
--- a/README.md
+++ b/README.md
@@ -5,8 +5,8 @@ Declarative package manager for Arch Linux that syncs your system with a declare
 ## Features
 
 - Declarative state management — define your desired package list in files or stdin
-- Smart orphan cleanup — removes packages no longer needed
-- Explicit package tracking — marks declared packages as explicit
+- Explicit package tracking — marks declared packages as explicit (with `--prune`)
+- Smart orphan cleanup — removes packages no longer needed (with `--prune`)
 - AUR support — builds and installs AUR packages automatically
 - Machine-readable output — perfect for scripting
 
@@ -67,8 +67,9 @@ contents are automatically included in the package list.
 | Flag | Alias | Description |
 |------|-------|-------------|
 | `--state` | `-s` | State file(s) to read package list from (can be used multiple times) |
-| `--nocheck` | | Skip safety check (allow significant package count reductions)
+| `--nocheck` | | Skip safety check (allow significant package count reductions) |
 | `--dry-run` | | Preview changes without applying them |
+| `--prune` | | Mark packages as explicit and cleanup orphans |
 | `--verbose` | `-v` | Enable verbose output |
 | `--help` | `-h` | Show help message |
 
@@ -79,8 +80,8 @@ contents are automatically included in the package list.
 3. **Categorize** — Check if packages are in official repos or AUR
 4. **Sync** — Install/update packages via pacman
 5. **Build** — Build and install AUR packages via makepkg
-6. **Mark** — Mark declared packages as explicit, all others as dependencies
-7. **Cleanup** — Remove orphaned packages
+6. **Mark** (with `--prune`) — Mark declared packages as explicit, all others as dependencies
+7. **Cleanup** (with `--prune`) — Remove orphaned packages
 
 ### Database Freshness
 
diff --git a/cmd/declpac/main.go b/cmd/declpac/main.go
index 0e685aa..ddabb6b 100644
--- a/cmd/declpac/main.go
+++ b/cmd/declpac/main.go
@@ -19,6 +19,7 @@ type Config struct {
 	StateFiles []string
 	NoCheck    bool
 	DryRun     bool
+	Prune      bool
 	Verbose    bool
 }
 
@@ -45,6 +46,11 @@ func main() {
 				Usage:       "Simulate the sync without making changes",
 				Destination: &cfg.DryRun,
 			},
+			&cli.BoolFlag{
+				Name:        "prune",
+				Usage:       "Mark packages and cleanup orphans",
+				Destination: &cfg.Prune,
+			},
 			&cli.BoolFlag{
 				Name:        "verbose",
 				Aliases:     []string{"v"},
@@ -97,7 +103,7 @@ func run(cfg *Config) error {
 	}
 	defer log.Close()
 
-	result, err := pacman.Sync(merged, cfg.NoCheck)
+	result, err := pacman.Sync(merged, cfg.NoCheck, cfg.Prune)
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "error: %v\n", err)
 		return err
diff --git a/pkg/pacman/pacman.go b/pkg/pacman/pacman.go
index 2d05981..a9a8586 100644
--- a/pkg/pacman/pacman.go
+++ b/pkg/pacman/pacman.go
@@ -13,7 +13,7 @@ import (
 	"github.com/Riyyi/declpac/pkg/pacman/sync"
 )
 
-func Sync(packages []string, noCheck bool) (*output.Result, error) {
+func Sync(packages []string, noCheck bool, prune bool) (*output.Result, error) {
 	start := time.Now()
 	log.Debug("Sync: starting...")
 
@@ -82,19 +82,24 @@ func Sync(packages []string, noCheck bool) (*output.Result, error) {
 		log.Debug("Sync: AUR package %s installed (%.2fs)", pkg, time.Since(start).Seconds())
 	}
 
-	log.Debug("Sync: marking all as deps...")
-	markAllAsDeps()
-	log.Debug("Sync: all marked as deps (%.2fs)", time.Since(start).Seconds())
+	var removed int
+	if prune {
+		log.Debug("Sync: marking all as deps...")
+		if err := markAllAsDeps(); err != nil {
+			return nil, err
+		}
+		log.Debug("Sync: all marked as deps (%.2fs)", time.Since(start).Seconds())
 
-	log.Debug("Sync: marking state packages as explicit...")
-	if err := sync.MarkAs(packages, "explicit", log.GetLogWriter()); err != nil {
-		fmt.Fprintf(os.Stderr, "warning: could not mark state packages as explicit: %v\n", err)
-	}
-	log.Debug("Sync: state packages marked as explicit (%.2fs)", time.Since(start).Seconds())
+		log.Debug("Sync: marking state packages as explicit...")
+		if err := sync.MarkAs(packages, "explicit", log.GetLogWriter()); err != nil {
+			fmt.Fprintf(os.Stderr, "warning: could not mark state packages as explicit: %v\n", err)
+		}
+		log.Debug("Sync: state packages marked as explicit (%.2fs)", time.Since(start).Seconds())
 
-	removed, err := cleanupOrphans()
-	if err != nil {
-		return nil, err
+		removed, err = cleanupOrphans()
+		if err != nil {
+			return nil, err
+		}
 	}
 
 	list, _ = read.List()