diff --git a/src/specify_cli/presets/_catalog.py b/src/specify_cli/presets/_catalog.py
index a4768cc22d..5d359ab685 100644
--- a/src/specify_cli/presets/_catalog.py
+++ b/src/specify_cli/presets/_catalog.py
@@ -2,6 +2,7 @@
 
 import hashlib
 import json
+import logging
 import os
 import tempfile
 from dataclasses import dataclass
@@ -20,6 +21,8 @@
 )
 from ._manifest import PresetError, PresetValidationError
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class PresetCatalogEntry:
@@ -302,18 +305,15 @@ def get_active_catalogs(self) -> List[PresetCatalogEntry]:
         Raises:
             PresetValidationError: If a catalog URL is invalid
         """
-        import sys
-
         # 1. SPECKIT_PRESET_CATALOG_URL env var replaces all defaults
         if env_value := os.environ.get("SPECKIT_PRESET_CATALOG_URL"):
             catalog_url = env_value.strip()
             self._validate_catalog_url(catalog_url)
             if catalog_url != self.DEFAULT_CATALOG_URL:
                 if not getattr(self, "_non_default_catalog_warning_shown", False):
-                    print(
-                        "Warning: Using non-default preset catalog. "
-                        "Only use catalogs from sources you trust.",
-                        file=sys.stderr,
+                    logger.warning(
+                        "Using non-default preset catalog. "
+                        "Only use catalogs from sources you trust."
                     )
                     self._non_default_catalog_warning_shown = True
             return [PresetCatalogEntry(url=catalog_url, name="custom", priority=1, install_allowed=True, description="Custom catalog via SPECKIT_PRESET_CATALOG_URL")]
diff --git a/tests/specify_cli/presets/test_catalog.py b/tests/specify_cli/presets/test_catalog.py
index 2ffbddfed9..343d4a5901 100644
--- a/tests/specify_cli/presets/test_catalog.py
+++ b/tests/specify_cli/presets/test_catalog.py
@@ -2,6 +2,7 @@
 
 import io
 import json
+import logging
 import tarfile
 import zipfile
 from contextlib import contextmanager
@@ -251,6 +252,42 @@ def test_env_var_catalog_url(self, project_dir, monkeypatch):
         catalog = PresetCatalog(project_dir)
         assert catalog.get_catalog_url() == "https://custom.example.com/catalog.json"
 
+    def test_non_default_catalog_url_warns_through_logger_once(
+        self, project_dir, monkeypatch, caplog, capsys
+    ):
+        """The override warning reaches the logging framework, not stderr.
+
+        Regresses the print(..., file=sys.stderr) implementation: that wrote
+        the message straight to stderr and logging captured nothing.
+        """
+        monkeypatch.setenv(
+            "SPECKIT_PRESET_CATALOG_URL", "https://custom.example.com/catalog.json"
+        )
+        catalog = PresetCatalog(project_dir)
+        caplog.set_level(logging.WARNING, logger="specify_cli.presets._catalog")
+
+        assert catalog.get_catalog_url() == "https://custom.example.com/catalog.json"
+
+        message = "Using non-default preset catalog"
+        assert message in caplog.text
+        assert message not in capsys.readouterr().err
+
+        # Once per catalog instance: a second lookup must not repeat it.
+        catalog.get_catalog_url()
+        assert caplog.text.count(message) == 1
+
+    def test_default_catalog_url_logs_no_warning(
+        self, project_dir, monkeypatch, caplog
+    ):
+        """The default path must not emit the override warning."""
+        monkeypatch.delenv("SPECKIT_PRESET_CATALOG_URL", raising=False)
+        catalog = PresetCatalog(project_dir)
+        caplog.set_level(logging.WARNING, logger="specify_cli.presets._catalog")
+
+        catalog.get_catalog_url()
+
+        assert "Using non-default preset catalog" not in caplog.text
+
     # --- _make_request / GitHub auth ---
 
     def test_make_request_no_token_no_auth_header(self, project_dir, monkeypatch):