diff --git a/python/private/py_executable.bzl b/python/private/py_executable.bzl
index ea00eed17b..4b770fead3 100644
--- a/python/private/py_executable.bzl
+++ b/python/private/py_executable.bzl
@@ -670,6 +670,7 @@ def _create_stage2_bootstrap(
             "%venv_rel_site_packages%": venv.venv_site_packages,
             "%venv_root%": venv.venv_root,
             "%workspace_name%": ctx.workspace_name,
+            "%coverage_instrumented%": str(int(ctx.configuration.coverage_enabled and ctx.coverage_instrumented())),
         },
         is_executable = True,
     )
diff --git a/python/private/stage2_bootstrap_template.py b/python/private/stage2_bootstrap_template.py
index 4d98b03846..e3e303b3b1 100644
--- a/python/private/stage2_bootstrap_template.py
+++ b/python/private/stage2_bootstrap_template.py
@@ -41,6 +41,9 @@
 # string otherwise.
 VENV_SITE_PACKAGES = "%venv_rel_site_packages%"
 
+# Whether we should generate coverage data.
+COVERAGE_INSTRUMENTED = "%coverage_instrumented%" == "1"
+
 # ===== Template substitutions end =====
 
 
@@ -319,11 +322,14 @@ def _maybe_collect_coverage(enable):
     # We need for coveragepy to use relative paths.  This can only be configured
     # using an rc file.
     rcfile_name = os.path.join(coverage_dir, ".coveragerc_{}".format(unique_id))
+    disable_warnings = ('disable_warnings = module-not-imported, no-data-collected'
+                        if COVERAGE_INSTRUMENTED else '')
     print_verbose_coverage("coveragerc file:", rcfile_name)
     with open(rcfile_name, "w") as rcfile:
         rcfile.write(
             f"""[run]
 relative_files = True
+{disable_warnings}
 source =
 \t{source}
 """