diff --git a/scripts/travis_doxygen.sh b/scripts/travis_doxygen.sh
index 78adcff3c13..359de72ff60 100755
--- a/scripts/travis_doxygen.sh
+++ b/scripts/travis_doxygen.sh
@@ -8,5 +8,9 @@ pip install --user unidiff
 if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
   $script_folder/run_diff.sh DOXYGEN HEAD~1 # Check for errors introduced in last commit
 else
-  $script_folder/run_diff.sh DOXYGEN $TRAVIS_BRANCH # Check for errors compared to merge target
+  TMP_HEAD=$(git rev-parse HEAD)
+  git config remote.origin.fetch +refs/heads/$TRAVIS_BRANCH:refs/remotes/origin/$TRAVIS_BRANCH
+  git fetch --unshallow
+  git checkout $TMP_HEAD
+  $script_folder/run_diff.sh DOXYGEN origin/$TRAVIS_BRANCH # Check for errors compared to merge target
 fi
diff --git a/scripts/travis_lint.sh b/scripts/travis_lint.sh
index 036605237ee..6592a3ebdfa 100755
--- a/scripts/travis_lint.sh
+++ b/scripts/travis_lint.sh
@@ -8,5 +8,9 @@ pip install --user unidiff
 if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
   $script_folder/run_diff.sh CPPLINT HEAD~1 # Check for errors introduced in last commit
 else
-  $script_folder/run_diff.sh CPPLINT $TRAVIS_BRANCH # Check for errors compared to merge target
+  TMP_HEAD=$(git rev-parse HEAD)
+  git config remote.origin.fetch +refs/heads/$TRAVIS_BRANCH:refs/remotes/origin/$TRAVIS_BRANCH
+  git fetch --unshallow
+  git checkout $TMP_HEAD
+  $script_folder/run_diff.sh CPPLINT origin/$TRAVIS_BRANCH # Check for errors compared to merge target
 fi