diff --git a/doctr/__main__.py b/doctr/__main__.py
index 86bcbe93..b652dc4b 100644
--- a/doctr/__main__.py
+++ b/doctr/__main__.py
@@ -45,6 +45,10 @@
 
 from . import __version__
 
+# Force all prints to flush to keep the output in order on Travis
+builtin_print = print
+print = lambda *args, **kwargs: builtin_print(*args, **{'flush': True, **kwargs})
+
 def make_parser_with_config_adder(parser, config):
     """factory function for a smarter parser:
 
diff --git a/doctr/travis.py b/doctr/travis.py
index 178032dc..4ae15eea 100644
--- a/doctr/travis.py
+++ b/doctr/travis.py
@@ -18,6 +18,10 @@
 from .common import red, blue
 DOCTR_WORKING_BRANCH = '__doctr_working_branch'
 
+# Force all prints to flush to keep the output in order on Travis
+builtin_print = print
+print = lambda *args, **kwargs: builtin_print(*args, **{'flush': True, **kwargs})
+
 def decrypt_file(file, key):
     """
     Decrypts the file ``file``.
@@ -148,6 +152,8 @@ def run(args, shell=False, exit=True):
     sys.stdout.flush()
 
     returncode = run_command_hiding_token(args, token, shell=shell)
+    sys.stdout.flush()
+    sys.stderr.flush()
 
     if exit and returncode != 0:
         sys.exit(red("%s failed: %s" % (command, returncode)))