diff --git a/src/jaxsim/logging.py b/src/jaxsim/logging.py
index 00dc56477..7e0e7fe8e 100644
--- a/src/jaxsim/logging.py
+++ b/src/jaxsim/logging.py
@@ -1,8 +1,45 @@
 import enum
+import inspect
 import logging
+import os
+import warnings
 
 import coloredlogs
 
+
+class JaxSimWarning(UserWarning):
+    pass
+
+
+_original_showwarning = warnings.showwarning
+_jaxsim_root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+
+
+def pretty_jaxsim_warning(message, category, filename, lineno, file=None, line=None):
+    try:
+        caller_frame = inspect.stack()[2]
+        caller_file = caller_frame.filename
+    except Exception:
+        caller_file = filename
+
+    if caller_file.startswith(_jaxsim_root_dir):
+        print(f"\033[93m⚠️  {category.__name__}:\033[0m {message}")
+        print(f"   → {filename}:{lineno}")
+    else:
+        _original_showwarning(message, category, filename, lineno, file, line)
+
+
+# Register filter & formatter only for JaxSimWarning
+# and configure it to show each warning only once
+warnings.showwarning = pretty_jaxsim_warning
+warnings.filterwarnings("once")
+
+
+# Utility function to issue a JaxSim warning
+def jaxsim_warn(msg):
+    warnings.warn(msg, category=JaxSimWarning, stacklevel=2)
+
+
 LOGGER_NAME = "jaxsim"
 
 
diff --git a/src/jaxsim/parsers/descriptions/model.py b/src/jaxsim/parsers/descriptions/model.py
index 6b3fdb02d..714df5791 100644
--- a/src/jaxsim/parsers/descriptions/model.py
+++ b/src/jaxsim/parsers/descriptions/model.py
@@ -5,6 +5,7 @@
 from collections.abc import Sequence
 
 from jaxsim import logging
+from jaxsim.logging import jaxsim_warn
 
 from ..kinematic_graph import KinematicGraph, KinematicGraphTransforms, RootPose
 from .collision import CollidablePoint, CollisionShape
@@ -164,7 +165,7 @@ def reduce(self, considered_joints: Sequence[str]) -> ModelDescription:
             A `ModelDescription` instance that only includes the considered joints.
         """
 
-        logging.warning(
+        jaxsim_warn(
             "The joint order in the model description is not preserved when reducing "
             "the model. Consider using the `names_to_indices` method to get the correct "
             "order of the joints, or use the `joint_names()` method to inspect the internal joint ordering."