diff --git a/nanobot/cli/stream.py b/nanobot/cli/stream.py
index 382ae9aac..899950fb6 100644
--- a/nanobot/cli/stream.py
+++ b/nanobot/cli/stream.py
@@ -18,6 +18,16 @@ from rich.markdown import Markdown
 from rich.text import Text
 
 
+def _clear_current_line(console: Console) -> None:
+    """Erase a transient status line before printing persistent output."""
+    file = console.file
+    isatty = getattr(file, "isatty", lambda: False)
+    if not isatty():
+        return
+    file.write("\r\x1b[2K")
+    file.flush()
+
+
 def _make_console() -> Console:
     """Create a Console that emits plain text when stdout is not a TTY.
 
@@ -37,6 +47,7 @@ class ThinkingSpinner:
 
     def __init__(self, console: Console | None = None, bot_name: str = "nanobot"):
         c = console or _make_console()
+        self._console = c
         self._spinner = c.status(f"[dim]{bot_name} is thinking...[/dim]", spinner="dots")
         self._active = False
 
@@ -48,6 +59,7 @@ class ThinkingSpinner:
     def __exit__(self, *exc):
         self._active = False
         self._spinner.stop()
+        _clear_current_line(self._console)
         return False
 
     def pause(self):
@@ -58,6 +70,7 @@ class ThinkingSpinner:
         def _ctx():
             if self._spinner and self._active:
                 self._spinner.stop()
+                _clear_current_line(self._console)
             try:
                 yield
             finally:
diff --git a/tests/cli/test_cli_input.py b/tests/cli/test_cli_input.py
index 8b7a79cfc..3f5619c4f 100644
--- a/tests/cli/test_cli_input.py
+++ b/tests/cli/test_cli_input.py
@@ -1,5 +1,6 @@
 import asyncio
 from contextlib import nullcontext
+from io import StringIO
 from unittest.mock import AsyncMock, MagicMock, call, patch
 
 import pytest
@@ -97,6 +98,23 @@ def test_print_cli_progress_line_pauses_spinner_before_printing():
     assert order == ["start", "stop", "print", "start", "stop"]
 
 
+def test_thinking_spinner_clears_status_line_when_paused():
+    """Stopping the spinner should erase its transient line before output."""
+    stream = StringIO()
+    stream.isatty = lambda: True  # type: ignore[method-assign]
+    mock_console = MagicMock()
+    mock_console.file = stream
+    spinner = MagicMock()
+    mock_console.status.return_value = spinner
+
+    thinking = stream_mod.ThinkingSpinner(console=mock_console)
+    with thinking:
+        with thinking.pause():
+            pass
+
+    assert "\r\x1b[2K" in stream.getvalue()
+
+
 def test_print_cli_progress_line_opens_renderer_header_before_trace():
     """Trace lines should appear under the assistant header, not under You."""
     order: list[str] = []