diff --git a/graphify/prs.py b/graphify/prs.py
index 9534e6c00..a1ef3b6c5 100644
--- a/graphify/prs.py
+++ b/graphify/prs.py
@@ -142,6 +142,7 @@ def _gh(*args: str) -> list | dict | None:
     try:
         result = subprocess.run(
             ["gh", *args],
+            stdin=subprocess.DEVNULL,
             # Decode gh's output as UTF-8, not the Windows cp1252 locale codec: gh
             # emits UTF-8 JSON with non-Latin1 titles/logins (emoji, فارسی), and the
             # default text=True decode crashes on those (#1505 fixed the same in llm).
@@ -157,24 +158,27 @@ def _gh(*args: str) -> list | dict | None:
 def _detect_default_branch(repo: str | None = None) -> str:
     """Auto-detect the repo's default branch via gh, then git, then fall back to 'main'."""
     # Try gh first — works for any repo, not just the current directory
-    args = ["repo", "view", "--json", "defaultBranchRef"]
+    args = ["repo", "view"]
     if repo:
-        args += ["--repo", repo]
+        args.append(repo)
+    args += ["--json", "defaultBranchRef"]
     data = _gh(*args)
     if data and data.get("defaultBranchRef", {}).get("name"):
         return data["defaultBranchRef"]["name"]
-    # Fall back to git symbolic-ref for the current repo
-    try:
-        result = subprocess.run(
-            ["git", "symbolic-ref", "refs/remotes/origin/HEAD"],
-            capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=5
-        )
-        if result.returncode == 0:
-            # refs/remotes/origin/main → main
-            ref = result.stdout.strip()
-            return ref.split("/")[-1] if ref else "main"
-    except (subprocess.TimeoutExpired, FileNotFoundError):
-        pass
+    # Fall back to git symbolic-ref for the current repo (only when repo is not specified)
+    if not repo:
+        try:
+            result = subprocess.run(
+                ["git", "symbolic-ref", "refs/remotes/origin/HEAD"],
+                stdin=subprocess.DEVNULL,
+                capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=5
+            )
+            if result.returncode == 0:
+                # refs/remotes/origin/main → main
+                ref = result.stdout.strip()
+                return ref.split("/")[-1] if ref else "main"
+        except (subprocess.TimeoutExpired, FileNotFoundError):
+            pass
     return "main"
 
 
@@ -232,7 +236,11 @@ def fetch_pr_files(number: int, repo: str | None = None) -> list[str]:
     if repo:
         args += ["--repo", repo]
     try:
-        result = subprocess.run(["gh", *args], capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=30)
+        result = subprocess.run(
+            ["gh", *args],
+            stdin=subprocess.DEVNULL,
+            capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=30
+        )
         if result.returncode != 0:
             return []
         return [l.strip() for l in result.stdout.splitlines() if l.strip()]
@@ -303,6 +311,7 @@ def fetch_worktrees() -> dict[str, str]:
     try:
         result = subprocess.run(
             ["git", "worktree", "list", "--porcelain"],
+            stdin=subprocess.DEVNULL,
             capture_output=True, text=True, encoding="utf-8", errors="replace", timeout=10
         )
         if result.returncode != 0:
diff --git a/tests/test_prs.py b/tests/test_prs.py
index 4acc343e6..2bf4e9154 100644
--- a/tests/test_prs.py
+++ b/tests/test_prs.py
@@ -376,6 +376,27 @@ class TestDetectDefaultBranch:
         ):
             assert _detect_default_branch() == "main"
 
+    def test_repo_positional_arg_in_gh_repo_view(self):
+        """gh repo view takes repo positionally; --repo is not a valid flag (#3318)."""
+        with patch(
+            "graphify.prs._gh",
+            return_value={"defaultBranchRef": {"name": "main"}},
+        ) as mock_gh:
+            branch = _detect_default_branch(repo="owner/repo")
+        assert branch == "main"
+        args, _ = mock_gh.call_args
+        assert args == ("repo", "view", "owner/repo", "--json", "defaultBranchRef")
+        assert "--repo" not in args
+
+    def test_explicit_repo_gh_fails_returns_main_without_local_git(self):
+        """When an explicit repo is supplied and gh fails, return 'main' without
+        inspecting the local repository (#3318)."""
+        with patch("graphify.prs._gh", return_value=None), \
+             patch("graphify.prs.subprocess.run") as mock_git:
+            branch = _detect_default_branch(repo="owner/repo")
+        assert branch == "main"
+        mock_git.assert_not_called()
+
 
 # ── build_community_labels ─────────────────────────────────────────────────────
 
@@ -462,3 +483,39 @@ class TestSubprocessOutputEncoding:
             _detect_default_branch()
         _args, kwargs = mock_run.call_args
         assert kwargs.get("encoding") == "utf-8"
+
+
+# ── Subprocess stdin isolation (#3318) ─────────────────────────────────────────
+
+class TestSubprocessStdinIsolation:
+    """Subprocesses in prs.py must isolate stdin with subprocess.DEVNULL so they
+    never inherit an open stdin pipe from the MCP stdio server (#3318)."""
+
+    def test_gh_passes_devnull_stdin(self):
+        completed = MagicMock(returncode=0, stdout="[]", stderr="")
+        with patch("subprocess.run", return_value=completed) as mock_run:
+            _gh("repo", "view")
+        _args, kwargs = mock_run.call_args
+        assert kwargs.get("stdin") == subprocess.DEVNULL
+
+    def test_fetch_pr_files_passes_devnull_stdin(self):
+        completed = MagicMock(returncode=0, stdout="", stderr="")
+        with patch("subprocess.run", return_value=completed) as mock_run:
+            fetch_pr_files(1)
+        _args, kwargs = mock_run.call_args
+        assert kwargs.get("stdin") == subprocess.DEVNULL
+
+    def test_fetch_worktrees_passes_devnull_stdin(self):
+        completed = MagicMock(returncode=0, stdout="", stderr="")
+        with patch("subprocess.run", return_value=completed) as mock_run:
+            fetch_worktrees()
+        _args, kwargs = mock_run.call_args
+        assert kwargs.get("stdin") == subprocess.DEVNULL
+
+    def test_detect_default_branch_git_fallback_passes_devnull_stdin(self):
+        completed = MagicMock(returncode=0, stdout="refs/remotes/origin/main\n", stderr="")
+        with patch("graphify.prs._gh", return_value=None), \
+             patch("subprocess.run", return_value=completed) as mock_run:
+            _detect_default_branch()
+        _args, kwargs = mock_run.call_args
+        assert kwargs.get("stdin") == subprocess.DEVNULL