diff --git a/backend/onyx/context/search/pipeline.py b/backend/onyx/context/search/pipeline.py
index f387642d80..c7bece314b 100644
--- a/backend/onyx/context/search/pipeline.py
+++ b/backend/onyx/context/search/pipeline.py
@@ -5,11 +5,13 @@ from typing import cast
 
 from sqlalchemy.orm import Session
 
+from onyx.chat.models import ContextualPruningConfig
 from onyx.chat.models import PromptConfig
 from onyx.chat.models import SectionRelevancePiece
 from onyx.chat.prune_and_merge import _merge_sections
 from onyx.chat.prune_and_merge import ChunkRange
 from onyx.chat.prune_and_merge import merge_chunk_intervals
+from onyx.chat.prune_and_merge import prune_and_merge_sections
 from onyx.configs.chat_configs import DISABLE_LLM_DOC_RELEVANCE
 from onyx.context.search.enums import LLMEvaluationType
 from onyx.context.search.enums import QueryFlow
@@ -61,6 +63,7 @@ class SearchPipeline:
         | None = None,
         rerank_metrics_callback: Callable[[RerankMetricsContainer], None] | None = None,
         prompt_config: PromptConfig | None = None,
+        contextual_pruning_config: ContextualPruningConfig | None = None,
     ):
         # NOTE: The Search Request contains a lot of fields that are overrides, many of them can be None
         # and typically are None. The preprocessing will fetch default values to replace these empty overrides.
@@ -77,6 +80,9 @@ class SearchPipeline:
         self.search_settings = get_current_search_settings(db_session)
         self.document_index = get_default_document_index(self.search_settings, None)
         self.prompt_config: PromptConfig | None = prompt_config
+        self.contextual_pruning_config: ContextualPruningConfig | None = (
+            contextual_pruning_config
+        )
 
         # Preprocessing steps generate this
         self._search_query: SearchQuery | None = None
@@ -420,7 +426,26 @@ class SearchPipeline:
         if self._final_context_sections is not None:
             return self._final_context_sections
 
-        self._final_context_sections = _merge_sections(sections=self.reranked_sections)
+        if (
+            self.contextual_pruning_config is not None
+            and self.prompt_config is not None
+        ):
+            self._final_context_sections = prune_and_merge_sections(
+                sections=self.reranked_sections,
+                section_relevance_list=None,
+                prompt_config=self.prompt_config,
+                llm_config=self.llm.config,
+                question=self.search_query.query,
+                contextual_pruning_config=self.contextual_pruning_config,
+            )
+
+        else:
+            logger.error(
+                "Contextual pruning or prompt config not set, using default merge"
+            )
+            self._final_context_sections = _merge_sections(
+                sections=self.reranked_sections
+            )
         return self._final_context_sections
 
     @property
diff --git a/backend/onyx/tools/tool_implementations/search/search_tool.py b/backend/onyx/tools/tool_implementations/search/search_tool.py
index 379b2dd2a9..08751e2119 100644
--- a/backend/onyx/tools/tool_implementations/search/search_tool.py
+++ b/backend/onyx/tools/tool_implementations/search/search_tool.py
@@ -376,6 +376,7 @@ class SearchTool(Tool[SearchToolOverrideKwargs]):
             db_session=alternate_db_session or self.db_session,
             prompt_config=self.prompt_config,
             retrieved_sections_callback=retrieved_sections_callback,
+            contextual_pruning_config=self.contextual_pruning_config,
         )
 
         search_query_info = SearchQueryInfo(
@@ -447,6 +448,7 @@ class SearchTool(Tool[SearchToolOverrideKwargs]):
             db_session=self.db_session,
             bypass_acl=self.bypass_acl,
             prompt_config=self.prompt_config,
+            contextual_pruning_config=self.contextual_pruning_config,
         )
 
         # Log what we're doing