diff --git a/dvc/repo/scm_context.py b/dvc/repo/scm_context.py
index b5985b117..6f189c597 100644
--- a/dvc/repo/scm_context.py
+++ b/dvc/repo/scm_context.py
@@ -2,6 +2,7 @@ def scm_context(method):
     def run(repo, *args, **kw):
         try:
             result = method(repo, *args, **kw)
+            repo.scm.reset_tracked_files()
             repo.scm.reset_ignores()
             repo.scm.remind_to_track()
             return result
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..04b42747d 100644
--- a/dvc/scm/git/__init__.py
+++ b/dvc/scm/git/__init__.py
@@ -245,6 +245,9 @@ class Git(Base):
     def reset_ignores(self):
         self.ignored_paths = []
 
+    def reset_tracked_files(self):
+        self.files_to_track = []
+
     def remind_to_track(self):
         if not self.files_to_track:
             return