diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index b44c0143..9fe20cba 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -5,6 +5,7 @@ Changelog
 Unreleased
 ----------
 
+* Change internal handling of loggers
 * Fix installation link in README
 
 v0.1.34 (2025-12-02)
diff --git a/src/mdacli/cli.py b/src/mdacli/cli.py
index 92190d88..310e16b1 100644
--- a/src/mdacli/cli.py
+++ b/src/mdacli/cli.py
@@ -10,7 +10,6 @@
 import logging
 import sys
 import traceback
-import warnings
 
 import argcomplete
 from MDAnalysis.analysis.base import AnalysisBase
@@ -27,8 +26,6 @@
 from .logger import setup_logging
 from .utils import _exit_if_a_is_b
 
-logger = logging.getLogger(__name__)
-
 
 def cli(
     name,
@@ -113,11 +110,8 @@ def cli(
 
     if args.debug:
         level = logging.DEBUG
-    else:
-        # Ignore all warnings if not in debug mode, because MDA is noisy
-        warnings.filterwarnings("ignore")
 
-    with setup_logging(logger, logfile=args.logfile, level=level):
+    with setup_logging(logfile=args.logfile, level=level):
         # Execute the main client interface.
         try:
             analysis_callable = args.analysis_callable
diff --git a/src/mdacli/libcli.py b/src/mdacli/libcli.py
index ecdada19..f1542bec 100644
--- a/src/mdacli/libcli.py
+++ b/src/mdacli/libcli.py
@@ -20,7 +20,6 @@
 import MDAnalysis as mda
 from MDAnalysis.transformations.boxdimensions import set_dimensions
 
-from .colors import Emphasise
 from .save import save
 from .utils import convert_str_time, parse_callable_signature, parse_docs
 
@@ -45,13 +44,6 @@
 }
 
 
-def _warning(message, *args, **kwargs):  # NOQA: ARG001
-    logger.warning(Emphasise.warning(message))
-
-
-warnings.showwarning = _warning
-
-
 class KwargsDict(argparse.Action):
     """Convert input string to a dictionary.
 
diff --git a/src/mdacli/logger.py b/src/mdacli/logger.py
index e851b41c..2057d1f7 100644
--- a/src/mdacli/logger.py
+++ b/src/mdacli/logger.py
@@ -48,7 +48,6 @@ def check_suffix(filename: str | Path, suffix: str) -> str | Path:
 
 @contextlib.contextmanager
 def setup_logging(
-    logobj: logging.Logger,
     logfile: str | Path | None = None,
     level: int = logging.WARNING,
 ):
@@ -67,9 +66,13 @@ def setup_logging(
         message logged from errors, warnings and infos will be displayed.
     """
     try:
-        format = ""
+        # Get the root logger
+        logobj = logging.getLogger()
+
         if level == logging.DEBUG:
-            format += "[{levelname}]:{filename}:{funcName}:{lineno} - "
+            format = "[{levelname}]:{filename}:{funcName}:{lineno} - "
+        else:
+            format = ""
         format += "{message}"
 
         formatter = logging.Formatter(format, style="{")
@@ -90,8 +93,11 @@ def setup_logging(
             logging.addLevelName(logging.WARNING, Emphasise.warning("WARNING"))
             logging.addLevelName(logging.ERROR, Emphasise.error("ERROR"))
 
-        logging.basicConfig(format=format, handlers=handlers, level=level, style="{")
-        logging.captureWarnings(True)
+        logobj.setLevel(level)
+        for handler in handlers:
+            handler.setLevel(level)
+            handler.setFormatter(formatter)
+            logobj.addHandler(handler)
 
         if logfile:
             abs_path = str(Path(logfile).absolute().resolve())
@@ -99,8 +105,8 @@ def setup_logging(
         else:
             logobj.debug("Logging to file is disabled.")
 
-        for handler in handlers:
-            logobj.addHandler(handler)
+        # Redirect warnings (from the warnings library) to the logging system
+        logging.captureWarnings(True)
 
         yield
 
diff --git a/tests/test_logger.py b/tests/test_logger.py
index 21bf4912..862e3a31 100644
--- a/tests/test_logger.py
+++ b/tests/test_logger.py
@@ -41,9 +41,7 @@ def test_warnings_in_log(caplog):
     Keep this test at the top since it seems otherwise there are some pytest
     issues...
     """
-    logger = logging.getLogger()
-
-    with setup_logging(logger):
+    with setup_logging():
         warnings.warn("A warning", stacklevel=1)
 
     assert "A warning" in caplog.text
@@ -54,7 +52,7 @@ def test_default_log(caplog, capsys):
     caplog.set_level(logging.INFO)
     logger = logging.getLogger()
 
-    with setup_logging(logger, level=logging.INFO):
+    with setup_logging(level=logging.INFO):
         logger.info("foo")
         logger.debug("A debug message")
 
@@ -72,7 +70,7 @@ def test_info_log(caplog, monkeypatch, tmp_path, capsys):
     caplog.set_level(logging.INFO)
     logger = logging.getLogger()
 
-    with setup_logging(logger, logfile="logfile.log", level=logging.INFO):
+    with setup_logging(logfile="logfile.log", level=logging.INFO):
         logger.info("foo")
         logger.debug("A debug message")
 
@@ -97,7 +95,7 @@ def test_debug_log(caplog, monkeypatch, tmp_path, capsys):
     caplog.set_level(logging.DEBUG)
     logger = logging.getLogger()
 
-    with setup_logging(logger, logfile="logfile.log", level=logging.DEBUG):
+    with setup_logging(logfile="logfile.log", level=logging.DEBUG):
         logger.info("foo")
         logger.debug("A debug message")