diff --git a/cibuildwheel/linux.py b/cibuildwheel/linux.py
index f22304c05..24008cdf6 100644
--- a/cibuildwheel/linux.py
+++ b/cibuildwheel/linux.py
@@ -306,18 +306,27 @@ def build(options: BuildOptions) -> None:
             log.step_end_with_error(
                 f"Command {error.cmd} failed with code {error.returncode}. {error.stdout}"
             )
-            troubleshoot(options.package_dir, error)
+            troubleshoot(options, error)
             sys.exit(1)
 
 
-def troubleshoot(package_dir: Path, error: Exception) -> None:
+def _matches_prepared_command(error_cmd: List[str], command_template: str) -> bool:
+    if len(error_cmd) < 3 or error_cmd[0:2] != ["sh", "-c"]:
+        return False
+    command_prefix = command_template.split("{", maxsplit=1)[0].strip()
+    return error_cmd[2].startswith(command_prefix)
+
+
+def troubleshoot(options: BuildOptions, error: Exception) -> None:
+
     if isinstance(error, subprocess.CalledProcessError) and (
         error.cmd[0:4] == ["python", "-m", "pip", "wheel"]
         or error.cmd[0:3] == ["python", "-m", "build"]
+        or _matches_prepared_command(error.cmd, options.repair_command)
     ):
         # the wheel build step failed
         print("Checking for common errors...")
-        so_files = list(package_dir.glob("**/*.so"))
+        so_files = list(options.package_dir.glob("**/*.so"))
 
         if so_files:
             print(
@@ -326,10 +335,17 @@ def troubleshoot(package_dir: Path, error: Exception) -> None:
                     NOTE: Shared object (.so) files found in this project.
 
                     These files might be built against the wrong OS, causing problems with
-                    auditwheel.
+                    auditwheel. If possible, run cibuildwheel in a clean checkout.
 
                     If you're using Cython and have previously done an in-place build,
                     remove those build files (*.so and *.c) before starting cibuildwheel.
+
+                    setuptools uses the build/ folder to store its build cache. It
+                    may be necessary to remove those build files (*.so and *.o) before
+                    starting cibuildwheel.
+
+                    Files that belong to a virtual environment are probably not an issue
+                    unless you used a custom command telling cibuildwheel to activate it.
                     """
                 ),
                 file=sys.stderr,
diff --git a/test/test_troubleshooting.py b/test/test_troubleshooting.py
index 6a58ca1fd..7039c2687 100644
--- a/test/test_troubleshooting.py
+++ b/test/test_troubleshooting.py
@@ -3,25 +3,23 @@
 import pytest
 
 from . import utils
-from .test_projects import TestProject
+from .test_projects import TestProject, new_c_project
 
-so_file_project = TestProject()
+SO_FILE_WARNING = "NOTE: Shared object (.so) files found in this project."
 
-so_file_project.files["libnothing.so"] = ""
 
-so_file_project.files[
-    "setup.py"
-] = """
-raise Exception('this build will fail')
-"""
+@pytest.mark.parametrize("project_contains_so_files", [False, True])
+def test_failed_build_with_so_files(tmp_path, capfd, build_frontend_env, project_contains_so_files):
+    project = TestProject()
+    project.files["setup.py"] = "raise Exception('this build will fail')\n"
+    if project_contains_so_files:
+        project.files["libnothing.so"] = ""
 
-
-def test_failed_project_with_so_files(tmp_path, capfd, build_frontend_env):
     if utils.platform != "linux":
         pytest.skip("this test is only relevant to the linux build")
 
     project_dir = tmp_path / "project"
-    so_file_project.generate(project_dir)
+    project.generate(project_dir)
 
     with pytest.raises(subprocess.CalledProcessError):
         utils.cibuildwheel_run(project_dir, add_env=build_frontend_env)
@@ -29,4 +27,34 @@ def test_failed_project_with_so_files(tmp_path, capfd, build_frontend_env):
     captured = capfd.readouterr()
     print("out", captured.out)
     print("err", captured.err)
-    assert "NOTE: Shared object (.so) files found in this project." in captured.err
+
+    if project_contains_so_files:
+        assert SO_FILE_WARNING in captured.err
+    else:
+        assert SO_FILE_WARNING not in captured.err
+
+
+@pytest.mark.parametrize("project_contains_so_files", [False, True])
+def test_failed_repair_with_so_files(tmp_path, capfd, project_contains_so_files):
+    if utils.platform != "linux":
+        pytest.skip("this test is only relevant to the linux build")
+
+    project = new_c_project()
+
+    if project_contains_so_files:
+        project.files["libnothing.so"] = ""
+
+    project_dir = tmp_path / "project"
+    project.generate(project_dir)
+
+    with pytest.raises(subprocess.CalledProcessError):
+        utils.cibuildwheel_run(project_dir, add_env={"CIBW_REPAIR_WHEEL_COMMAND": "false"})
+
+    captured = capfd.readouterr()
+    print("out", captured.out)
+    print("err", captured.err)
+
+    if project_contains_so_files:
+        assert SO_FILE_WARNING in captured.err
+    else:
+        assert SO_FILE_WARNING not in captured.err