diff --git a/dffs/utils.py b/dffs/utils.py
index ac7e784..b38a05b 100644
--- a/dffs/utils.py
+++ b/dffs/utils.py
@@ -5,6 +5,7 @@
 from os.path import relpath
 from subprocess import Popen, PIPE
 from sys import stdout
+from threading import Thread
 
 from utz import err, named_pipes, pipeline, process
 
@@ -87,8 +88,22 @@ def join_pipelines(
             pipe1,
             pipe2,
         ]
-        # Capture stdout so we can suppress it if a pipeline fails
+        # Capture stdout so we can suppress it if a pipeline fails.
+        # Drain in a background thread — otherwise, when `base_cmd`'s output
+        # exceeds the pipe buffer (~64 KB on Linux) it blocks writing, which
+        # blocks it from reading the FIFOs, which blocks the pipelines'
+        # writes, which blocks the `p.wait()` calls below → deadlock.
         proc = Popen(join_cmd, stdout=PIPE)
+        drain: dict[str, bytes | BaseException] = {}
+
+        def drain_stdout() -> None:
+            try:
+                drain['out'] = proc.stdout.read() if proc.stdout else b''
+            except BaseException as e:  # surface, don't silently truncate
+                drain['err'] = e
+
+        stdout_thread = Thread(target=drain_stdout, daemon=True)
+        stdout_thread.start()
 
         # Track pipeline processes and their commands
         pipeline_groups = []  # List of (cmds, procs) tuples
@@ -149,9 +164,12 @@ def join_pipelines(
                             stderr_output = stderr_output.decode('utf-8', errors='replace')
                         err(stderr_output.rstrip())
 
-        # Wait for base_cmd and capture its output
+        # Wait for base_cmd; the drain thread already has its output.
         proc.wait()
-        base_stdout = proc.stdout.read() if proc.stdout else b''
+        stdout_thread.join()
+        if 'err' in drain:
+            raise drain['err']
+        base_stdout = drain.get('out', b'')
 
         # If any pipeline failed, suppress base_cmd output and return error code
         if pipeline_failed:
diff --git a/tests/test_join_pipelines.py b/tests/test_join_pipelines.py
index f60f5af..ad6c723 100644
--- a/tests/test_join_pipelines.py
+++ b/tests/test_join_pipelines.py
@@ -1,4 +1,7 @@
 """Tests for join_pipelines function."""
+import signal
+from io import StringIO
+
 import pytest
 from dffs.utils import join_pipelines
 
@@ -190,3 +193,53 @@ def test_shell_false_multi_stage(self):
             shell=False,
         )
         assert returncode == 0
+
+
+class TestJoinPipelinesLargeOutput:
+    """Regression: previously, `join_pipelines` captured `base_cmd`'s stdout
+    via `stdout=PIPE` and only read it after `p.wait()` returned for each
+    pipeline. When `base_cmd`'s output exceeded the pipe buffer (~64 KB on
+    Linux), the writer blocked, which stopped it from draining the FIFOs the
+    pipelines wrote to, which blocked `p.wait()` → deadlock. Fixed by draining
+    `base_cmd`'s stdout in a background thread."""
+
+    def test_large_diff_output_does_not_deadlock(self, monkeypatch):
+        """Diff of two ≥100 KB-per-side streams that fully differ produces
+        several hundred KB of diff output — well over the pipe buffer. Must
+        complete promptly (a broken fix hangs indefinitely) *and* emit the
+        full output (a truncating drain would silently drop lines)."""
+        # `join_pipelines` writes to the module-level `stdout` it bound at
+        # import (`from sys import stdout`), so capture that object directly —
+        # `capsys`/`capfd` don't see writes through this stale reference.
+        buf = StringIO()
+        monkeypatch.setattr('dffs.utils.stdout', buf)
+
+        def _timeout(signum, frame):
+            raise TimeoutError("join_pipelines deadlocked on large output")
+        prev = signal.signal(signal.SIGALRM, _timeout)
+        signal.alarm(10)  # fix completes in <1 s; 10 s is generous
+        try:
+            # `seq 1 30000` ≈ 169 KB per side; differing content ⇒ full diff
+            # (~340 KB output) — comfortably over the 64 KB pipe buffer.
+            returncode = join_pipelines(
+                base_cmd=['diff'],
+                cmds1=['seq 1 30000'],
+                cmds2=['seq 30001 60000'],
+                shell=True,
+            )
+        finally:
+            signal.alarm(0)
+            signal.signal(signal.SIGALRM, prev)
+        # Files differ ⇒ diff exits 1.
+        assert returncode == 1
+        # Disjoint sequences ⇒ diff replaces every line of side 1 with every
+        # line of side 2: one `c` hunk header, then all 30000 `<` lines, a
+        # `---` separator, then all 30000 `>` lines. Asserting the full lists
+        # verifies the drain thread captured every byte, not a truncated head.
+        out_lines = buf.getvalue().rstrip("\n").split("\n")
+        assert out_lines[0] == "1,30000c1,30000"
+        assert [l[2:] for l in out_lines if l.startswith("< ")] == \
+            [str(i) for i in range(1, 30001)]
+        assert out_lines[30001] == "---"
+        assert [l[2:] for l in out_lines if l.startswith("> ")] == \
+            [str(i) for i in range(30001, 60001)]