diff --git a/integrations/pinecone/src/haystack_integrations/document_stores/pinecone/document_store.py b/integrations/pinecone/src/haystack_integrations/document_stores/pinecone/document_store.py
index 422fb12605..3b06eec4ea 100644
--- a/integrations/pinecone/src/haystack_integrations/document_stores/pinecone/document_store.py
+++ b/integrations/pinecone/src/haystack_integrations/document_stores/pinecone/document_store.py
@@ -1,6 +1,7 @@
 # SPDX-FileCopyrightText: 2023-present deepset GmbH <info@deepset.ai>
 #
 # SPDX-License-Identifier: Apache-2.0
+
 from copy import copy
 from typing import Any, Literal, Optional, Union
 
@@ -376,6 +377,165 @@ async def delete_all_documents_async(self) -> None:
             # Namespace doesn't exist (empty collection), which is fine - nothing to delete
             logger.debug("Namespace '{namespace}' not found. Nothing to delete.", namespace=self.namespace or "default")
 
+    @staticmethod
+    def _update_documents_metadata(documents: list[Document], meta: dict[str, Any]) -> None:
+        """
+        Updates metadata for a list of documents by merging the provided meta dictionary.
+
+        :param documents: List of documents to update.
+        :param meta: Metadata fields to merge into each document's existing metadata.
+        """
+        for document in documents:
+            if document.meta is None:
+                document.meta = {}
+            document.meta.update(meta)
+
+    def delete_by_filter(self, filters: dict[str, Any]) -> int:
+        """
+        Deletes all documents that match the provided filters.
+
+        Pinecone does not support server-side delete by filter, so this method
+        first searches for matching documents, then deletes them by ID.
+
+        :param filters: The filters to apply to select documents for deletion.
+            For filter syntax, see [Haystack metadata filtering](https://docs.haystack.deepset.ai/docs/metadata-filtering)
+        :returns: The number of documents deleted.
+        """
+        _validate_filters(filters)
+
+        self._initialize_index()
+        assert self._index is not None, "Index is not initialized"
+
+        documents = self.filter_documents(filters=filters)
+        if not documents:
+            return 0
+
+        document_ids = [doc.id for doc in documents]
+
+        self.delete_documents(document_ids)
+
+        deleted_count = len(document_ids)
+        logger.info(
+            "Deleted {n_docs} documents from index '{index}' using filters.",
+            n_docs=deleted_count,
+            index=self.index_name,
+        )
+
+        return deleted_count
+
+    async def delete_by_filter_async(self, filters: dict[str, Any]) -> int:
+        """
+        Asynchronously deletes all documents that match the provided filters.
+
+        Pinecone does not support server-side delete by filter, so this method
+        first searches for matching documents, then deletes them by ID.
+
+        :param filters: The filters to apply to select documents for deletion.
+            For filter syntax, see [Haystack metadata filtering](https://docs.haystack.deepset.ai/docs/metadata-filtering)
+        :returns: The number of documents deleted.
+        """
+        _validate_filters(filters)
+
+        await self._initialize_async_index()
+        assert self._async_index is not None, "Index is not initialized"
+
+        documents = await self.filter_documents_async(filters=filters)
+        if not documents:
+            return 0
+
+        document_ids = [doc.id for doc in documents]
+
+        await self.delete_documents_async(document_ids)
+
+        deleted_count = len(document_ids)
+        logger.info(
+            "Deleted {n_docs} documents from index '{index}' using filters.",
+            n_docs=deleted_count,
+            index=self.index_name,
+        )
+
+        return deleted_count
+
+    def update_by_filter(self, filters: dict[str, Any], meta: dict[str, Any]) -> int:
+        """
+        Updates the metadata of all documents that match the provided filters.
+
+        Pinecone does not support server-side update by filter, so this method
+        first searches for matching documents, then updates their metadata and re-writes them.
+
+        :param filters: The filters to apply to select documents for updating.
+            For filter syntax, see [Haystack metadata filtering](https://docs.haystack.deepset.ai/docs/metadata-filtering)
+        :param meta: The metadata fields to update. This will be merged with existing metadata.
+        :returns: The number of documents updated.
+        """
+        _validate_filters(filters)
+
+        if not isinstance(meta, dict):
+            msg = "meta must be a dictionary"
+            raise ValueError(msg)
+
+        self._initialize_index()
+        assert self._index is not None, "Index is not initialized"
+
+        documents = self.filter_documents(filters=filters)
+        if not documents:
+            return 0
+
+        self._update_documents_metadata(documents, meta)
+
+        # Re-write documents with updated metadata
+        # Using OVERWRITE policy to update existing documents
+        self.write_documents(documents, policy=DuplicatePolicy.OVERWRITE)
+
+        updated_count = len(documents)
+        logger.info(
+            "Updated {n_docs} documents in index '{index}' using filters.",
+            n_docs=updated_count,
+            index=self.index_name,
+        )
+
+        return updated_count
+
+    async def update_by_filter_async(self, filters: dict[str, Any], meta: dict[str, Any]) -> int:
+        """
+        Asynchronously updates the metadata of all documents that match the provided filters.
+
+        Pinecone does not support server-side update by filter, so this method
+        first searches for matching documents, then updates their metadata and re-writes them.
+
+        :param filters: The filters to apply to select documents for updating.
+            For filter syntax, see [Haystack metadata filtering](https://docs.haystack.deepset.ai/docs/metadata-filtering)
+        :param meta: The metadata fields to update. This will be merged with existing metadata.
+        :returns: The number of documents updated.
+        """
+        _validate_filters(filters)
+
+        if not isinstance(meta, dict):
+            msg = "meta must be a dictionary"
+            raise ValueError(msg)
+
+        await self._initialize_async_index()
+        assert self._async_index is not None, "Index is not initialized"
+
+        documents = await self.filter_documents_async(filters=filters)
+        if not documents:
+            return 0
+
+        self._update_documents_metadata(documents, meta)
+
+        # Re-write documents with updated metadata
+        # Using OVERWRITE policy to update existing documents
+        await self.write_documents_async(documents, policy=DuplicatePolicy.OVERWRITE)
+
+        updated_count = len(documents)
+        logger.info(
+            "Updated {n_docs} documents in index '{index}' using filters.",
+            n_docs=updated_count,
+            index=self.index_name,
+        )
+
+        return updated_count
+
     def _embedding_retrieval(
         self,
         query_embedding: list[float],
diff --git a/integrations/pinecone/tests/test_document_store.py b/integrations/pinecone/tests/test_document_store.py
index 152ac436d4..6d6e8d577e 100644
--- a/integrations/pinecone/tests/test_document_store.py
+++ b/integrations/pinecone/tests/test_document_store.py
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2023-present deepset GmbH <info@deepset.ai>
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import os
 import time
 from unittest.mock import patch
@@ -342,3 +346,100 @@ def test_sentence_window_retriever(self, document_store: PineconeDocumentStore):
         result = sentence_window_retriever.run(retrieved_documents=[retrieved_doc["documents"][0]])
 
         assert len(result["context_windows"]) == 1
+
+    def test_delete_by_filter(self, document_store: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A"}),
+            Document(content="Doc 2", meta={"category": "B"}),
+            Document(content="Doc 3", meta={"category": "A"}),
+        ]
+        document_store.write_documents(docs)
+
+        # delete documents with category="A"
+        deleted_count = document_store.delete_by_filter(
+            filters={"field": "meta.category", "operator": "==", "value": "A"}
+        )
+        assert deleted_count == 2
+        assert document_store.count_documents() == 1
+
+        # verify only category B remains
+        remaining_docs = document_store.filter_documents()
+        assert len(remaining_docs) == 1
+        assert remaining_docs[0].meta["category"] == "B"
+
+    def test_delete_by_filter_no_matches(self, document_store: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A"}),
+            Document(content="Doc 2", meta={"category": "B"}),
+        ]
+        document_store.write_documents(docs)
+
+        # try to delete documents with category="C" (no matches)
+        deleted_count = document_store.delete_by_filter(
+            filters={"field": "meta.category", "operator": "==", "value": "C"}
+        )
+        assert deleted_count == 0
+        assert document_store.count_documents() == 2
+
+    def test_update_by_filter(self, document_store: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A", "status": "draft"}),
+            Document(content="Doc 2", meta={"category": "B", "status": "draft"}),
+            Document(content="Doc 3", meta={"category": "A", "status": "draft"}),
+        ]
+        document_store.write_documents(docs)
+
+        # update status for category="A" documents
+        updated_count = document_store.update_by_filter(
+            filters={"field": "meta.category", "operator": "==", "value": "A"}, meta={"status": "published"}
+        )
+        assert updated_count == 2
+
+        published_docs = document_store.filter_documents(
+            filters={"field": "meta.status", "operator": "==", "value": "published"}
+        )
+        assert len(published_docs) == 2
+        for doc in published_docs:
+            assert doc.meta["category"] == "A"
+            assert doc.meta["status"] == "published"
+
+    def test_update_by_filter_multiple_fields(self, document_store: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A", "status": "draft", "priority": "low"}),
+            Document(content="Doc 2", meta={"category": "B", "status": "draft", "priority": "low"}),
+            Document(content="Doc 3", meta={"category": "A", "status": "draft", "priority": "low"}),
+        ]
+        document_store.write_documents(docs)
+        assert document_store.count_documents() == 3
+
+        # Update multiple fields for category="A" documents
+        updated_count = document_store.update_by_filter(
+            filters={"field": "meta.category", "operator": "==", "value": "A"},
+            meta={"status": "published", "priority": "high"},
+        )
+        assert updated_count == 2
+
+        # Verify the updates
+        published_docs = document_store.filter_documents(
+            filters={"field": "meta.status", "operator": "==", "value": "published"}
+        )
+        assert len(published_docs) == 2
+        for doc in published_docs:
+            assert doc.meta["category"] == "A"
+            assert doc.meta["status"] == "published"
+            assert doc.meta["priority"] == "high"
+
+    def test_update_by_filter_no_matches(self, document_store: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A"}),
+            Document(content="Doc 2", meta={"category": "B"}),
+        ]
+        document_store.write_documents(docs)
+        assert document_store.count_documents() == 2
+
+        # Try to update documents with category="C" (no matches)
+        updated_count = document_store.update_by_filter(
+            filters={"field": "meta.category", "operator": "==", "value": "C"}, meta={"status": "published"}
+        )
+        assert updated_count == 0
+        assert document_store.count_documents() == 2
diff --git a/integrations/pinecone/tests/test_document_store_async.py b/integrations/pinecone/tests/test_document_store_async.py
index 60f1abed54..6832ddf819 100644
--- a/integrations/pinecone/tests/test_document_store_async.py
+++ b/integrations/pinecone/tests/test_document_store_async.py
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2023-present deepset GmbH <info@deepset.ai>
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import os
 
 import numpy as np
@@ -139,3 +143,99 @@ async def test_sentence_window_retriever(self, document_store_async: PineconeDoc
         result = sentence_window_retriever.run(retrieved_documents=[retrieved_doc["documents"][0]])
 
         assert len(result["context_windows"]) == 1
+
+    async def test_delete_by_filter_async(self, document_store_async: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A"}),
+            Document(content="Doc 2", meta={"category": "B"}),
+            Document(content="Doc 3", meta={"category": "A"}),
+        ]
+        await document_store_async.write_documents_async(docs)
+
+        # delete documents with category="A"
+        deleted_count = await document_store_async.delete_by_filter_async(
+            filters={"field": "meta.category", "operator": "==", "value": "A"}
+        )
+        assert deleted_count == 2
+        assert await document_store_async.count_documents_async() == 1
+
+        # only category B remains
+        remaining_docs = await document_store_async.filter_documents_async()
+        assert len(remaining_docs) == 1
+        assert remaining_docs[0].meta["category"] == "B"
+
+    async def test_delete_by_filter_async_no_matches(self, document_store_async: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A"}),
+            Document(content="Doc 2", meta={"category": "B"}),
+        ]
+        await document_store_async.write_documents_async(docs)
+
+        # delete documents with category="C" (no matches)
+        deleted_count = await document_store_async.delete_by_filter_async(
+            filters={"field": "meta.category", "operator": "==", "value": "C"}
+        )
+        assert deleted_count == 0
+        assert await document_store_async.count_documents_async() == 2
+
+    async def test_update_by_filter_async(self, document_store_async: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A", "status": "draft"}),
+            Document(content="Doc 2", meta={"category": "B", "status": "draft"}),
+            Document(content="Doc 3", meta={"category": "A", "status": "draft"}),
+        ]
+        await document_store_async.write_documents_async(docs)
+        assert await document_store_async.count_documents_async() == 3
+
+        # update status for category="A" documents
+        updated_count = await document_store_async.update_by_filter_async(
+            filters={"field": "meta.category", "operator": "==", "value": "A"}, meta={"status": "published"}
+        )
+        assert updated_count == 2
+
+        published_docs = await document_store_async.filter_documents_async(
+            filters={"field": "meta.status", "operator": "==", "value": "published"}
+        )
+        assert len(published_docs) == 2
+        for doc in published_docs:
+            assert doc.meta["category"] == "A"
+            assert doc.meta["status"] == "published"
+
+    async def test_update_by_filter_async_multiple_fields(self, document_store_async: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A", "status": "draft", "priority": "low"}),
+            Document(content="Doc 2", meta={"category": "B", "status": "draft", "priority": "low"}),
+            Document(content="Doc 3", meta={"category": "A", "status": "draft", "priority": "low"}),
+        ]
+        await document_store_async.write_documents_async(docs)
+
+        # update multiple fields for category="A" documents
+        updated_count = await document_store_async.update_by_filter_async(
+            filters={"field": "meta.category", "operator": "==", "value": "A"},
+            meta={"status": "published", "priority": "high"},
+        )
+        assert updated_count == 2
+
+        # verify the updates
+        published_docs = await document_store_async.filter_documents_async(
+            filters={"field": "meta.status", "operator": "==", "value": "published"}
+        )
+        assert len(published_docs) == 2
+        for doc in published_docs:
+            assert doc.meta["category"] == "A"
+            assert doc.meta["status"] == "published"
+            assert doc.meta["priority"] == "high"
+
+    async def test_update_by_filter_async_no_matches(self, document_store_async: PineconeDocumentStore):
+        docs = [
+            Document(content="Doc 1", meta={"category": "A"}),
+            Document(content="Doc 2", meta={"category": "B"}),
+        ]
+        await document_store_async.write_documents_async(docs)
+
+        # try to update documents with category="C" (no matches)
+        updated_count = await document_store_async.update_by_filter_async(
+            filters={"field": "meta.category", "operator": "==", "value": "C"}, meta={"status": "published"}
+        )
+        assert updated_count == 0
+        assert await document_store_async.count_documents_async() == 2