diff --git a/augur/__main__.py b/augur/__main__.py
index d69eae231..59f89dd8f 100644
--- a/augur/__main__.py
+++ b/augur/__main__.py
@@ -14,11 +14,21 @@ def main():
 
         # Explicitly enable universal newlines mode so we do the right thing.
         newline=None,
+
+        # By default, stdout is line-buffered when interactive (e.g. for
+        # consistent stdio interleaving) but block-buffered when not for (I
+        # assume) better performance.
     )
     # Apply the above to stderr as well.
     sys.stderr.reconfigure(
         errors="backslashreplace",
         newline=None,
+
+        # Always line-buffer stderr since we only use it for messaging, not
+        # data output.  This is the Python default from 3.9 onwards, but we
+        # also run on 3.8 where it's not.  Be consistent regardless of Python
+        # version.
+        line_buffering=True,
     )
 
     return augur.run( argv[1:] )