diff --git a/Makefile b/Makefile
index 4ba74ac8f..b690907ec 100644
--- a/Makefile
+++ b/Makefile
@@ -18,13 +18,13 @@ tests:
 
 .PHONY: coverage
 coverage:
-	uv run coverage run -m pytest tests -m "not integration"
+	uv run coverage run --omit="src/mcp_agent/cli/**" -m pytest tests -m "not integration"
 	uv run coverage xml -o coverage.xml
 	uv run coverage report -m --fail-under=80
 
 .PHONY: coverage-report
 coverage-report:
-	uv run coverage run -m pytest tests
+	uv run coverage run --omit="src/mcp_agent/cli/**" -m pytest tests
 	uv run coverage html
 
 .PHONY: schema