diff --git a/integrations/pinecone/examples/example.py b/integrations/pinecone/examples/example.py
index a10b951b5..71d289ef6 100644
--- a/integrations/pinecone/examples/example.py
+++ b/integrations/pinecone/examples/example.py
@@ -15,6 +15,7 @@
 from haystack.components.embedders import SentenceTransformersDocumentEmbedder, SentenceTransformersTextEmbedder
 from haystack.components.preprocessors import DocumentSplitter
 from haystack.components.writers import DocumentWriter
+from haystack.utils import Secret
 
 from haystack_integrations.components.retrievers.pinecone import PineconeEmbeddingRetriever
 from haystack_integrations.document_stores.pinecone import PineconeDocumentStore
@@ -22,7 +23,11 @@
 file_paths = glob.glob("neural-search-pills/pills/*.md")
 
 document_store = PineconeDocumentStore(
-    api_key="YOUR-PINECONE-API-KEY", environment="gcp-starter", index="default", namespace="default", dimension=768
+    api_key=Secret.from_token("YOUR-PINECONE-API-KEY"),
+    environment="gcp-starter",
+    index="default",
+    namespace="default",
+    dimension=768,
 )
 
 indexing = Pipeline()
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 92ea987b4..91364d7bf 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
@@ -3,14 +3,14 @@
 # SPDX-License-Identifier: Apache-2.0
 import io
 import logging
-import os
 from copy import copy
 from typing import Any, Dict, List, Optional
 
 import pandas as pd
-from haystack import default_to_dict
+from haystack import default_from_dict, default_to_dict
 from haystack.dataclasses import Document
 from haystack.document_stores.types import DuplicatePolicy
+from haystack.utils import Secret, deserialize_secrets_inplace
 from haystack.utils.filters import convert
 
 import pinecone
@@ -29,7 +29,7 @@ class PineconeDocumentStore:
     def __init__(
         self,
         *,
-        api_key: Optional[str] = None,
+        api_key: Secret = Secret.from_env_var("PINECONE_API_KEY"),  # noqa: B008
         environment: str = "us-west1-gcp",
         index: str = "default",
         namespace: str = "default",
@@ -58,15 +58,16 @@ def __init__(
             [API reference](https://docs.pinecone.io/reference/create_index-1).
 
         """
-        api_key = api_key or os.environ.get("PINECONE_API_KEY")
-        if not api_key:
+        resolved_api_key = api_key.resolve_value()
+        if resolved_api_key is None:
             msg = (
                 "PineconeDocumentStore expects an API key. "
                 "Set the PINECONE_API_KEY environment variable (recommended) or pass it explicitly."
             )
             raise ValueError(msg)
+        self.api_key = api_key
 
-        pinecone.init(api_key=api_key, environment=environment)
+        pinecone.init(api_key=resolved_api_key, environment=environment)
 
         if index not in pinecone.list_indexes():
             logger.info(f"Index {index} does not exist. Creating a new index.")
@@ -92,9 +93,15 @@ def __init__(
         self.batch_size = batch_size
         self.index_creation_kwargs = index_creation_kwargs
 
+    @classmethod
+    def from_dict(cls, data: Dict[str, Any]) -> "PineconeDocumentStore":
+        deserialize_secrets_inplace(data["init_parameters"], keys=["api_key"])
+        return default_from_dict(cls, data)
+
     def to_dict(self) -> Dict[str, Any]:
         return default_to_dict(
             self,
+            api_key=self.api_key.to_dict(),
             environment=self.environment,
             index=self.index,
             dimension=self.dimension,
diff --git a/integrations/pinecone/tests/conftest.py b/integrations/pinecone/tests/conftest.py
index c7a1342d5..872b38a07 100644
--- a/integrations/pinecone/tests/conftest.py
+++ b/integrations/pinecone/tests/conftest.py
@@ -2,6 +2,7 @@
 
 import pytest
 from haystack.document_stores.types import DuplicatePolicy
+from pinecone.core.client.exceptions import NotFoundException
 
 from haystack_integrations.document_stores.pinecone import PineconeDocumentStore
 
@@ -51,4 +52,7 @@ def delete_documents_and_wait(filters):
     store.delete_documents = delete_documents_and_wait
 
     yield store
-    store._index.delete(delete_all=True, namespace=namespace)
+    try:
+        store._index.delete(delete_all=True, namespace=namespace)
+    except NotFoundException:
+        pass
diff --git a/integrations/pinecone/tests/test_document_store.py b/integrations/pinecone/tests/test_document_store.py
index cd1bb0db3..d8e8ace35 100644
--- a/integrations/pinecone/tests/test_document_store.py
+++ b/integrations/pinecone/tests/test_document_store.py
@@ -4,6 +4,7 @@
 import pytest
 from haystack import Document
 from haystack.testing.document_store import CountDocumentsTest, DeleteDocumentsTest, WriteDocumentsTest
+from haystack.utils import Secret
 
 from haystack_integrations.document_stores.pinecone import PineconeDocumentStore
 
@@ -13,7 +14,7 @@ def test_init(mock_pinecone):
     mock_pinecone.Index.return_value.describe_index_stats.return_value = {"dimension": 30}
 
     document_store = PineconeDocumentStore(
-        api_key="fake-api-key",
+        api_key=Secret.from_token("fake-api-key"),
         environment="gcp-starter",
         index="my_index",
         namespace="test",
@@ -34,7 +35,7 @@ def test_init(mock_pinecone):
 
 @patch("haystack_integrations.document_stores.pinecone.document_store.pinecone")
 def test_init_api_key_in_environment_variable(mock_pinecone, monkeypatch):
-    monkeypatch.setenv("PINECONE_API_KEY", "fake-api-key")
+    monkeypatch.setenv("PINECONE_API_KEY", "env-api-key")
 
     PineconeDocumentStore(
         environment="gcp-starter",
@@ -45,14 +46,14 @@ def test_init_api_key_in_environment_variable(mock_pinecone, monkeypatch):
         metric="euclidean",
     )
 
-    mock_pinecone.init.assert_called_with(api_key="fake-api-key", environment="gcp-starter")
+    mock_pinecone.init.assert_called_with(api_key="env-api-key", environment="gcp-starter")
 
 
 @patch("haystack_integrations.document_stores.pinecone.document_store.pinecone")
-def test_to_dict(mock_pinecone):
+def test_to_dict(mock_pinecone, monkeypatch):
     mock_pinecone.Index.return_value.describe_index_stats.return_value = {"dimension": 30}
+    monkeypatch.setenv("PINECONE_API_KEY", "env-api-key")
     document_store = PineconeDocumentStore(
-        api_key="fake-api-key",
         environment="gcp-starter",
         index="my_index",
         namespace="test",
@@ -63,6 +64,13 @@ def test_to_dict(mock_pinecone):
     assert document_store.to_dict() == {
         "type": "haystack_integrations.document_stores.pinecone.document_store.PineconeDocumentStore",
         "init_parameters": {
+            "api_key": {
+                "env_vars": [
+                    "PINECONE_API_KEY",
+                ],
+                "strict": True,
+                "type": "env_var",
+            },
             "environment": "gcp-starter",
             "index": "my_index",
             "dimension": 30,
@@ -85,12 +93,13 @@ def test_write_documents_duplicate_fail(self, document_store: PineconeDocumentSt
     @pytest.mark.skip(reason="Pinecone only supports UPSERT operations")
     def test_write_documents_duplicate_skip(self, document_store: PineconeDocumentStore): ...
 
+    @pytest.mark.skip(reason="Pinecone creates a namespace only when the first document is written")
+    def test_delete_documents_empty_document_store(self, document_store: PineconeDocumentStore): ...
+
     def test_init_fails_wo_api_key(self, monkeypatch):
-        api_key = None
         monkeypatch.delenv("PINECONE_API_KEY", raising=False)
         with pytest.raises(ValueError):
             PineconeDocumentStore(
-                api_key=api_key,
                 environment="gcp-starter",
                 index="my_index",
             )
diff --git a/integrations/pinecone/tests/test_emebedding_retriever.py b/integrations/pinecone/tests/test_emebedding_retriever.py
index d2d3c8546..9dc1c9760 100644
--- a/integrations/pinecone/tests/test_emebedding_retriever.py
+++ b/integrations/pinecone/tests/test_emebedding_retriever.py
@@ -18,10 +18,10 @@ def test_init_default():
 
 
 @patch("haystack_integrations.document_stores.pinecone.document_store.pinecone")
-def test_to_dict(mock_pinecone):
+def test_to_dict(mock_pinecone, monkeypatch):
+    monkeypatch.setenv("PINECONE_API_KEY", "env-api-key")
     mock_pinecone.Index.return_value.describe_index_stats.return_value = {"dimension": 512}
     document_store = PineconeDocumentStore(
-        api_key="test-key",
         environment="gcp-starter",
         index="default",
         namespace="test-namespace",
@@ -35,6 +35,13 @@ def test_to_dict(mock_pinecone):
         "init_parameters": {
             "document_store": {
                 "init_parameters": {
+                    "api_key": {
+                        "env_vars": [
+                            "PINECONE_API_KEY",
+                        ],
+                        "strict": True,
+                        "type": "env_var",
+                    },
                     "environment": "gcp-starter",
                     "index": "default",
                     "namespace": "test-namespace",