diff --git a/dvc/repo/scm_context.py b/dvc/repo/scm_context.py
index b5985b117..c0b0ffb5b 100644
--- a/dvc/repo/scm_context.py
+++ b/dvc/repo/scm_context.py
@@ -4,6 +4,7 @@ def scm_context(method):
             result = method(repo, *args, **kw)
             repo.scm.reset_ignores()
             repo.scm.remind_to_track()
+            repo.scm.reset_tracked_files()
             return result
         except Exception:
             repo.scm.cleanup_ignores()
diff --git a/dvc/scm/base.py b/dvc/scm/base.py
index d7f5333e3..e52fafe99 100644
--- a/dvc/scm/base.py
+++ b/dvc/scm/base.py
@@ -126,6 +126,11 @@ class Base(object):
         Method to reset in-memory ignore storing mechanism.
         """
 
+    def reset_tracked_files(self):
+        """
+        Method to reset in-memory tracked files storing mechanism.
+        """
+
     def remind_to_track(self):
         """
         Method to remind user to track newly created files handled by scm
diff --git a/dvc/scm/git/__init__.py b/dvc/scm/git/__init__.py
index 339e64339..c0592e896 100644
--- a/dvc/scm/git/__init__.py
+++ b/dvc/scm/git/__init__.py
@@ -54,7 +54,7 @@ class Git(Base):
         self.git.git.update_environment(LD_LIBRARY_PATH=libpath)
 
         self.ignored_paths = []
-        self.files_to_track = []
+        self.files_to_track = set()
 
     @staticmethod
     def is_repo(root_dir):
@@ -245,6 +245,9 @@ class Git(Base):
     def reset_ignores(self):
         self.ignored_paths = []
 
+    def reset_tracked_files(self):
+        self.files_to_track = set()
+
     def remind_to_track(self):
         if not self.files_to_track:
             return
@@ -257,7 +260,7 @@ class Git(Base):
         )
 
     def track_file(self, path):
-        self.files_to_track.append(path)
+        self.files_to_track.add(path)
 
     def belongs_to_scm(self, path):
         basename = os.path.basename(path)