diff --git a/cmd/db_cleanup.go b/cmd/db_cleanup.go
index 13a17575..e43b9ce4 100644
--- a/cmd/db_cleanup.go
+++ b/cmd/db_cleanup.go
@@ -143,6 +143,10 @@ func aptlyDbCleanup(cmd *commander.Command, args []string) error {
 
 		context.progress.Printf("Disk space freed: %.2f GiB...\n", float64(totalSize)/1024.0/1024.0/1024.0)
 	}
+
+	context.progress.Printf("Compacting database...\n")
+	err = context.database.CompactDB()
+
 	return err
 }
 
diff --git a/database/leveldb.go b/database/leveldb.go
index 5c42ec9f..deac8dea 100644
--- a/database/leveldb.go
+++ b/database/leveldb.go
@@ -7,6 +7,7 @@ import (
 	"github.com/syndtr/goleveldb/leveldb"
 	"github.com/syndtr/goleveldb/leveldb/filter"
 	"github.com/syndtr/goleveldb/leveldb/opt"
+	"github.com/syndtr/goleveldb/leveldb/util"
 )
 
 // Errors for Storage
@@ -24,6 +25,7 @@ type Storage interface {
 	Close() error
 	StartBatch()
 	FinishBatch() error
+	CompactDB() error
 }
 
 type levelDB struct {
@@ -49,6 +51,7 @@ func OpenDB(path string) (Storage, error) {
 	return &levelDB{db: db}, nil
 }
 
+// Get key value from database
 func (l *levelDB) Get(key []byte) ([]byte, error) {
 	value, err := l.db.Get(key, nil)
 	if err != nil {
@@ -61,6 +64,7 @@ func (l *levelDB) Get(key []byte) ([]byte, error) {
 	return value, nil
 }
 
+// Put saves key to database, if key has the same value in DB already, it is not saved
 func (l *levelDB) Put(key []byte, value []byte) error {
 	if l.batch != nil {
 		l.batch.Put(key, value)
@@ -79,6 +83,7 @@ func (l *levelDB) Put(key []byte, value []byte) error {
 	return l.db.Put(key, value, nil)
 }
 
+// Delete removes key from DB
 func (l *levelDB) Delete(key []byte) error {
 	if l.batch != nil {
 		l.batch.Delete(key)
@@ -87,6 +92,7 @@ func (l *levelDB) Delete(key []byte) error {
 	return l.db.Delete(key, nil)
 }
 
+// KeysByPrefix returns all keys that start with prefix
 func (l *levelDB) KeysByPrefix(prefix []byte) [][]byte {
 	result := make([][]byte, 0, 20)
 
@@ -103,6 +109,7 @@ func (l *levelDB) KeysByPrefix(prefix []byte) [][]byte {
 	return result
 }
 
+// FetchByPrefix returns all values with keys that start with prefix
 func (l *levelDB) FetchByPrefix(prefix []byte) [][]byte {
 	result := make([][]byte, 0, 20)
 
@@ -119,10 +126,14 @@ func (l *levelDB) FetchByPrefix(prefix []byte) [][]byte {
 	return result
 }
 
+// Close finishes DB work
 func (l *levelDB) Close() error {
 	return l.db.Close()
 }
 
+// StartBatch starts batch processing of keys
+//
+// All subsequent Get, Put and Delete would work on batch
 func (l *levelDB) StartBatch() {
 	if l.batch != nil {
 		panic("batch already started")
@@ -130,6 +141,7 @@ func (l *levelDB) StartBatch() {
 	l.batch = new(leveldb.Batch)
 }
 
+// FinishBatch finalizes the batch, saving operations
 func (l *levelDB) FinishBatch() error {
 	if l.batch == nil {
 		panic("no batch")
@@ -138,3 +150,8 @@ func (l *levelDB) FinishBatch() error {
 	l.batch = nil
 	return err
 }
+
+// CompactDB compacts database by merging layers
+func (l *levelDB) CompactDB() error {
+	return l.db.CompactRange(util.Range{})
+}
diff --git a/database/leveldb_test.go b/database/leveldb_test.go
index a93dc9aa..5863b456 100644
--- a/database/leveldb_test.go
+++ b/database/leveldb_test.go
@@ -122,3 +122,11 @@ func (s *LevelDBSuite) TestBatch(c *C) {
 	s.db.StartBatch()
 	c.Check(func() { s.db.StartBatch() }, Panics, "batch already started")
 }
+
+func (s *LevelDBSuite) TestCompactDB(c *C) {
+	s.db.Put([]byte{0x80, 0x01}, []byte{0x01})
+	s.db.Put([]byte{0x80, 0x03}, []byte{0x03})
+	s.db.Put([]byte{0x80, 0x02}, []byte{0x02})
+
+	c.Check(s.db.CompactDB(), IsNil)
+}
diff --git a/system/t08_db/CleanupDB1Test_gold b/system/t08_db/CleanupDB1Test_gold
index 11a05b46..1816ebdd 100644
--- a/system/t08_db/CleanupDB1Test_gold
+++ b/system/t08_db/CleanupDB1Test_gold
@@ -4,3 +4,4 @@ Deleting unreferenced packages (0)...
 Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (0)...
+Compacting database...
diff --git a/system/t08_db/CleanupDB2Test_gold b/system/t08_db/CleanupDB2Test_gold
index 061b8199..051152a6 100644
--- a/system/t08_db/CleanupDB2Test_gold
+++ b/system/t08_db/CleanupDB2Test_gold
@@ -4,3 +4,4 @@ Deleting unreferenced packages (73295)...
 Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (0)...
+Compacting database...
diff --git a/system/t08_db/CleanupDB3Test_gold b/system/t08_db/CleanupDB3Test_gold
index 1b003922..82c8446e 100644
--- a/system/t08_db/CleanupDB3Test_gold
+++ b/system/t08_db/CleanupDB3Test_gold
@@ -5,3 +5,4 @@ Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (9)...
 Disk space freed: 0.01 GiB...
+Compacting database...
diff --git a/system/t08_db/CleanupDB4Test_gold b/system/t08_db/CleanupDB4Test_gold
index 11a05b46..1816ebdd 100644
--- a/system/t08_db/CleanupDB4Test_gold
+++ b/system/t08_db/CleanupDB4Test_gold
@@ -4,3 +4,4 @@ Deleting unreferenced packages (0)...
 Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (0)...
+Compacting database...
diff --git a/system/t08_db/CleanupDB5Test_gold b/system/t08_db/CleanupDB5Test_gold
index 1b003922..82c8446e 100644
--- a/system/t08_db/CleanupDB5Test_gold
+++ b/system/t08_db/CleanupDB5Test_gold
@@ -5,3 +5,4 @@ Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (9)...
 Disk space freed: 0.01 GiB...
+Compacting database...
diff --git a/system/t08_db/CleanupDB6Test_gold b/system/t08_db/CleanupDB6Test_gold
index 11a05b46..1816ebdd 100644
--- a/system/t08_db/CleanupDB6Test_gold
+++ b/system/t08_db/CleanupDB6Test_gold
@@ -4,3 +4,4 @@ Deleting unreferenced packages (0)...
 Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (0)...
+Compacting database...
diff --git a/system/t08_db/CleanupDB7Test_gold b/system/t08_db/CleanupDB7Test_gold
index 11a05b46..1816ebdd 100644
--- a/system/t08_db/CleanupDB7Test_gold
+++ b/system/t08_db/CleanupDB7Test_gold
@@ -4,3 +4,4 @@ Deleting unreferenced packages (0)...
 Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (0)...
+Compacting database...
diff --git a/system/t08_db/CleanupDB8Test_gold b/system/t08_db/CleanupDB8Test_gold
index 8ab0e68b..4f43418e 100644
--- a/system/t08_db/CleanupDB8Test_gold
+++ b/system/t08_db/CleanupDB8Test_gold
@@ -5,3 +5,4 @@ Building list of files referenced by packages...
 Building list of files in package pool...
 Deleting unreferenced files (5)...
 Disk space freed: 0.00 GiB...
+Compacting database...