diff --git a/deb/publish.go b/deb/publish.go
index 79c47cb83..dbcc9eafd 100644
--- a/deb/publish.go
+++ b/deb/publish.go
@@ -17,6 +17,7 @@ import (
 
 	"github.com/aptly-dev/aptly/aptly"
 	"github.com/aptly-dev/aptly/database"
+	"github.com/aptly-dev/aptly/files"
 	"github.com/aptly-dev/aptly/pgp"
 	"github.com/aptly-dev/aptly/utils"
 )
@@ -1323,14 +1324,20 @@ func (collection *PublishedRepoCollection) Remove(publishedStorageProvider aptly
 	collection.list[len(collection.list)-1], collection.list[repoPosition], collection.list =
 		nil, collection.list[len(collection.list)-1], collection.list[:len(collection.list)-1]
 
-	if !skipCleanup && len(cleanComponents) > 0 {
-		err = collection.CleanupPrefixComponentFiles(repo.Prefix, cleanComponents,
-			publishedStorageProvider.GetPublishedStorage(storage), collectionFactory, progress)
-		if err != nil {
-			if !force {
-				return fmt.Errorf("cleanup failed, use -force-drop to override: %s", err)
+	if !skipCleanup {
+		publishedStorage := publishedStorageProvider.GetPublishedStorage(storage)
+		if len(cleanComponents) > 0 {
+			err = collection.CleanupPrefixComponentFiles(repo.Prefix, cleanComponents, publishedStorage, collectionFactory, progress)
+			if err != nil {
+				if !force {
+					return fmt.Errorf("cleanup failed, use -force-drop to override: %s", err)
+				}
 			}
 		}
+
+		if localStorage, ok := publishedStorage.(*files.PublishedStorage); ok {
+			localStorage.CleanupPublishTree(repo.Prefix)
+		}
 	}
 
 	batch := collection.db.CreateBatch()
diff --git a/files/public.go b/files/public.go
index 848f0c23c..c3cbbb8e3 100644
--- a/files/public.go
+++ b/files/public.go
@@ -119,6 +119,26 @@ func (storage *PublishedStorage) RemoveDirs(path string, progress aptly.Progress
 	return os.RemoveAll(filepath)
 }
 
+// Cleans up PublishedStorage tree towards the root up to first non-empty directory
+func (storage *PublishedStorage) CleanupPublishTree(path string) {
+	/*
+		Say, `path` is "a/b/c/d", let's remove all empty dirs:
+		 storage.rootPath + "a/b/c/d"
+		 storage.rootPath + "a/b/c"
+		 storage.rootPath + "a/b"
+		 ... and so on, up to first non-empty directory (or any other os.Remove error)
+	*/
+	segments := strings.Split(path, "/")
+
+	for segmentsCount := len(segments); segmentsCount > 0; segmentsCount-- {
+		err := os.Remove(filepath.Join(storage.rootPath, strings.Join(segments[:segmentsCount], "/")))
+
+		if err != nil {
+			break
+		}
+	}
+}
+
 // LinkFromPool links package file from pool to dist's pool location
 //
 // publishedPrefix is desired prefix for the location in the pool.
diff --git a/system/t06_publish/PublishDrop21Test_gold b/system/t06_publish/PublishDrop21Test_gold
new file mode 100644
index 000000000..c3758e105
--- /dev/null
+++ b/system/t06_publish/PublishDrop21Test_gold
@@ -0,0 +1,4 @@
+Removing ${HOME}/.aptly/public/ppa/smira/dists...
+Removing ${HOME}/.aptly/public/ppa/smira/pool...
+
+Published repository has been removed successfully.
diff --git a/system/t06_publish/drop.py b/system/t06_publish/drop.py
index 3c361cc31..f69020624 100644
--- a/system/t06_publish/drop.py
+++ b/system/t06_publish/drop.py
@@ -25,6 +25,7 @@ def check(self):
 class PublishDrop2Test(BaseTest):
     """
     publish drop: under prefix
+    if remaining tree is empty, it is now removed
     """
     requiresGPG2 = True
     fixtureDB = True
@@ -39,9 +40,33 @@ class PublishDrop2Test(BaseTest):
     def check(self):
         super(PublishDrop2Test, self).check()
 
-        self.check_not_exists('public/ppa/smira/dists/')
-        self.check_not_exists('public/ppa/smira/pool/')
-        self.check_exists('public/ppa/smira/')
+        self.check_not_exists('public/ppa/')
+        self.check_exists('public/')
+
+
+class PublishDrop21Test(BaseTest):
+    """
+    publish drop: under prefix
+    if some publishes have common part of the prefix, only empty parts are cleared
+    (https://github.com/aptly-dev/aptly/pull/1381)
+    """
+    requiresGPG2 = True
+    fixtureDB = True
+    fixturePool = True
+    fixtureCmds = [
+        "aptly snapshot create snap1 from mirror gnuplot-maverick",
+        "aptly snapshot create snap2 from mirror gnuplot-maverick",
+        "aptly publish snapshot -keyring=${files}/aptly.pub -secret-keyring=${files}/aptly.sec snap1 ppa/smira",
+        "aptly publish snapshot -keyring=${files}/aptly.pub -secret-keyring=${files}/aptly.sec snap2 ppa/another",
+    ]
+    runCmd = "aptly publish drop maverick ppa/smira"
+    gold_processor = BaseTest.expand_environ
+
+    def check(self):
+        super(PublishDrop21Test, self).check()
+
+        self.check_not_exists('public/ppa/smira/')
+        self.check_exists('public/ppa/another')
 
 
 class PublishDrop3Test(BaseTest):
@@ -132,6 +157,7 @@ class PublishDrop6Test(BaseTest):
 class PublishDrop7Test(BaseTest):
     """
     publish drop: under prefix with trailing & leading slashes
+    see comment in PublishDrop2Test
     """
     requiresGPG2 = True
     fixtureDB = True
@@ -148,7 +174,8 @@ def check(self):
 
         self.check_not_exists('public/ppa/smira/dists/')
         self.check_not_exists('public/ppa/smira/pool/')
-        self.check_exists('public/ppa/smira/')
+        self.check_not_exists('public/ppa/smira/')
+        self.check_exists('public/')
 
 
 class PublishDrop8Test(BaseTest):