diff --git a/ykman/_cli/__main__.py b/ykman/_cli/__main__.py
index 66951d72..d89f40db 100644
--- a/ykman/_cli/__main__.py
+++ b/ykman/_cli/__main__.py
@@ -272,7 +272,7 @@ def cli(ctx, device, log_level, log_file, reader):
     ctx.obj = YkmanContextObject()
 
     if log_level:
-        init_logging(log_level, log_file=log_file)
+        init_logging(log_level, log_file=log_file, replace=log_file is None)
         logger.info("\n".join(pretty_print({"System info": sys_info()})))
     elif log_file:
         ctx.fail("--log-file requires specifying --log-level.")
@@ -435,6 +435,7 @@ def main():
             msg = "An unexpected error has occurred"
             formatter.show_trace = True
         logger.exception(msg)
+        logging.shutdown()
         sys.exit(status)
 
 
diff --git a/ykman/logging.py b/ykman/logging.py
index 481da3e4..81cbeeac 100644
--- a/ykman/logging.py
+++ b/ykman/logging.py
@@ -64,13 +64,26 @@ def set_log_level(level: LOG_LEVEL):
         logger.warning(_print_box(*DEBUG_WARNING))
 
 
-def init_logging(log_level: LOG_LEVEL, log_file=None):
-    logging.basicConfig(
-        force=log_file is None,  # Replace the default logger if logging to stderr
-        datefmt="%H:%M:%S",
-        filename=log_file,
-        format="%(levelname)s %(asctime)s.%(msecs)d [%(name)s.%(funcName)s:%(lineno)d] "
+def init_logging(log_level: LOG_LEVEL, log_file=None, replace=False):
+    formatter = logging.Formatter(
+        "%(levelname)s %(asctime)s.%(msecs)d [%(name)s.%(funcName)s:%(lineno)d] "
         "%(message)s",
+        "%H:%M:%S",
+        "%",
     )
+    if log_file:
+        handler: logging.Handler = logging.FileHandler(log_file)
+    else:
+        handler = logging.StreamHandler()
+    handler.setFormatter(formatter)
 
+    root = logging.getLogger()
+    if replace:
+        for h in root.handlers[:]:
+            root.removeHandler(h)
+
+    root.addHandler(handler)
     set_log_level(log_level)
+
+    if log_file:
+        logger.warning(f"Logging to file: {log_file}")
diff --git a/ykman/logging_setup.py b/ykman/logging_setup.py
index ad01147e..941c9b52 100644
--- a/ykman/logging_setup.py
+++ b/ykman/logging_setup.py
@@ -32,6 +32,7 @@
 from datetime import datetime
 import platform
 import logging
+import warnings
 import ctypes
 import sys
 import os
@@ -55,7 +56,11 @@ def log_sys_info(log):
 
 
 def setup(log_level_name, log_file=None):
-    log_level = LOG_LEVEL[log_level_name.upper()]
-    init_logging(log_level, log_file=log_file)
+    warnings.warn(
+        "logging_setup.setup is deprecated, use logging.init_loging instead",
+        DeprecationWarning,
+    )
 
+    log_level = LOG_LEVEL[log_level_name.upper()]
+    init_logging(log_level, log_file=log_file, replace=log_file is None)
     log_sys_info(logger.debug)