diff --git a/src/cleveragents/application/container.py b/src/cleveragents/application/container.py
index 4af42bb4..9c99d39a 100644
--- a/src/cleveragents/application/container.py
+++ b/src/cleveragents/application/container.py
@@ -880,6 +880,14 @@ def get_container() -> Container:
     """
     global _container, _audit_subscriber_initialized
     if _container is None:
+        # Configure structlog before creating the container so that
+        # plugin_manager extension-point registration debug messages go to
+        # the Python logging infrastructure (respecting the WARNING threshold)
+        # rather than structlog's default PrintLoggerFactory which writes to
+        # stdout and pollutes machine-readable CLI output formats.
+        from cleveragents.config.logging import configure_structlog
+
+        configure_structlog(log_level="WARNING")
         _container = Container()
     # Retry audit subscriber initialization on every call until it
     # succeeds.  Previously, a failed attempt during the first
diff --git a/src/cleveragents/cli/main.py b/src/cleveragents/cli/main.py
index 2eb8fd82..58a3639b 100644
--- a/src/cleveragents/cli/main.py
+++ b/src/cleveragents/cli/main.py
@@ -307,6 +307,12 @@ def main_callback(
     ),
 ) -> None:
     """CleverAgents - AI-powered development assistant."""
+    # Suppress debug-level logs on stdout for ALL commands so machine-readable
+    # output formats (json, yaml, plain) receive clean stdout.  Commands that
+    # need verbose logging can override this after parsing --log-level flags.
+    from cleveragents.config.logging import configure_structlog
+
+    configure_structlog(log_level="WARNING")
     _register_subcommands()
 
 
@@ -659,6 +665,14 @@ def main(args: list[str] | None = None) -> int:
     Returns:
         Exit code (0 for success, non-zero for errors)
     """
+    # Configure structlog at the earliest possible point so that debug-level
+    # plugin_manager logs (emitted during module import) go to stderr and not
+    # stdout.  This ensures machine-readable output (--format json/yaml/plain)
+    # is not polluted with log lines.
+    from cleveragents.config.logging import configure_structlog
+
+    configure_structlog(log_level="WARNING")
+
     try:
         err_console = get_err_console()