diff --git a/haystack/tools/pipeline_tool.py b/haystack/tools/pipeline_tool.py
index 0c0b6e1397..2152b5bbc2 100644
--- a/haystack/tools/pipeline_tool.py
+++ b/haystack/tools/pipeline_tool.py
@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
+import copy
 from typing import Any, Callable
 
 from haystack import AsyncPipeline, Pipeline, SuperComponent, logging
@@ -221,7 +222,8 @@ def from_dict(cls, data: dict[str, Any]) -> "PipelineTool":
         :returns:
             The deserialized PipelineTool instance.
         """
-        inner_data = data["data"]
+        # Create a deep copy to avoid mutating the input dictionary
+        inner_data = copy.deepcopy(data["data"])
         is_pipeline_async = inner_data.get("is_pipeline_async", False)
         pipeline_class = AsyncPipeline if is_pipeline_async else Pipeline
         pipeline = pipeline_class.from_dict(inner_data["pipeline"])