diff --git a/sdks/python/apache_beam/options/pipeline_options.py b/sdks/python/apache_beam/options/pipeline_options.py
index 55fb2f1703fc6..626a906f8a094 100644
--- a/sdks/python/apache_beam/options/pipeline_options.py
+++ b/sdks/python/apache_beam/options/pipeline_options.py
@@ -556,7 +556,10 @@ def _add_argparse_args(cls, parser):
         action='store_true',
         help='Whether to automatically generate unique transform labels '
         'for every transform. The default behavior is to raise an '
-        'exception if a transform is created with a non-unique label.')
+        'exception if a transform is created with a non-unique label. '
+        'Using --auto_unique_labels could cause data loss when '
+        'updating a pipeline or reloading the job state. '
+        'This is not recommended for streaming jobs.')
 
 
 class StreamingOptions(PipelineOptions):
diff --git a/sdks/python/apache_beam/pipeline.py b/sdks/python/apache_beam/pipeline.py
index a20fae2ae735c..128ab9206bfd4 100644
--- a/sdks/python/apache_beam/pipeline.py
+++ b/sdks/python/apache_beam/pipeline.py
@@ -694,6 +694,10 @@ def apply(
       if auto_unique_labels:
         # If auto_unique_labels is set, we will append a unique suffix to the
         # label to make it unique.
+        logging.warning(
+            'Using --auto_unique_labels could cause data loss when '
+            'updating a pipeline or reloading the job state. '
+            'This is not recommended for streaming jobs.')
         unique_label = self._generate_unique_label(transform)
         return self.apply(transform, pvalueish, unique_label)
       else:
@@ -702,7 +706,10 @@ def apply(
             'To apply a transform with a specified label, write '
             'pvalue | "label" >> transform or use the option '
             '"auto_unique_labels" to automatically generate unique '
-            'transform labels' % full_label)
+            'transform labels. Note "auto_unique_labels" '
+            'could cause data loss when updating a pipeline or '
+            'reloading the job state. This is not recommended for '
+            'streaming jobs.' % full_label)
     self.applied_labels.add(full_label)
 
     pvalueish, inputs = transform._extract_input_pvalues(pvalueish)
diff --git a/sdks/python/apache_beam/pipeline_test.py b/sdks/python/apache_beam/pipeline_test.py
index 8d6cf4aceea01..b11211668e900 100644
--- a/sdks/python/apache_beam/pipeline_test.py
+++ b/sdks/python/apache_beam/pipeline_test.py
@@ -267,7 +267,10 @@ def test_reuse_custom_transform_instance(self):
         'pipeline. To apply a transform with a specified label, write '
         'pvalue | "label" >> transform or use the option '
         '"auto_unique_labels" to automatically generate unique '
-        'transform labels')
+        'transform labels. Note "auto_unique_labels" '
+        'could cause data loss when updating a pipeline or '
+        'reloading the job state. This is not recommended for '
+        'streaming jobs.')
 
   def test_auto_unique_labels(self):