diff --git a/semantica/pipeline/pipeline_builder.py b/semantica/pipeline/pipeline_builder.py
index d2044cbe..c64d5e64 100644
--- a/semantica/pipeline/pipeline_builder.py
+++ b/semantica/pipeline/pipeline_builder.py
@@ -272,7 +272,19 @@ class PipelineBuilder:
                 step_name = step_config.get("name")
                 step_type = step_config.get("type")
                 if step_name and step_type:
-                    self.add_step(step_name, step_type, **step_config.get("config", {}))
+                    step = self.add_step(
+                        step_name, step_type, **step_config.get("config", {})
+                    )
+                    step.dependencies = list(
+                        step_config.get("dependencies", step.dependencies)
+                    )
+                    step.delta_mode = step_config.get("delta_mode", step.delta_mode)
+                    step.base_version_id = step_config.get(
+                        "base_version_id", step.base_version_id
+                    )
+                    step.target_version_id = step_config.get(
+                        "target_version_id", step.target_version_id
+                    )
 
             # Set parallelism if specified
             if "parallelism" in pipeline_config:
@@ -398,14 +410,29 @@ class PipelineSerializer:
 
         Returns:
             Serialized pipeline
+
+        Notes:
+            Step handlers are runtime callables and are intentionally omitted from
+            the serialized representation. They must be rebound after deserialization.
         """
+        reserved_config_keys = {
+            "handler",
+            "dependencies",
+            "delta_mode",
+            "base_version_id",
+            "target_version_id",
+        }
         pipeline_data = {
             "name": pipeline.name,
             "steps": [
                 {
                     "name": step.name,
                     "type": step.step_type,
-                    "config": step.config,
+                    "config": {
+                        key: value
+                        for key, value in step.config.items()
+                        if key not in reserved_config_keys
+                    },
                     "dependencies": step.dependencies,
                     "delta_mode": getattr(step, "delta_mode", False),
                     "base_version_id": getattr(step, "base_version_id", None),
@@ -445,6 +472,18 @@ class PipelineSerializer:
         else:
             pipeline_data = serialized_pipeline
 
+        # Runtime handlers are process-local and cannot be reconstructed safely
+        # from serialized data. Copy before sanitizing so dict inputs are not mutated.
+        pipeline_data = dict(pipeline_data)
+        sanitized_steps = []
+        for step_data in pipeline_data.get("steps", []):
+            sanitized_step = dict(step_data)
+            step_config = dict(sanitized_step.get("config", {}))
+            step_config.pop("handler", None)
+            sanitized_step["config"] = step_config
+            sanitized_steps.append(sanitized_step)
+        pipeline_data["steps"] = sanitized_steps
+
         # Reconstruct pipeline
         builder = PipelineBuilder(**self.config)
         pipeline = builder.build_pipeline(pipeline_data, **options)
diff --git a/tests/pipeline/test_pipeline_serializer.py b/tests/pipeline/test_pipeline_serializer.py
new file mode 100644
index 00000000..fe616ddd
--- /dev/null
+++ b/tests/pipeline/test_pipeline_serializer.py
@@ -0,0 +1,103 @@
+import copy
+import json
+
+import pytest
+
+from semantica.pipeline.pipeline_builder import PipelineBuilder, PipelineSerializer
+
+
+@pytest.mark.parametrize("serialization_format", ["dict", "json"])
+def test_roundtrip_preserves_dependencies_and_delta_metadata(serialization_format):
+    builder = PipelineBuilder()
+    builder.add_step("extract", "source")
+    builder.add_step(
+        "index",
+        "sink",
+        delta_mode=True,
+        base_version_id="v1",
+        target_version_id="v2",
+    )
+    builder.connect_steps("extract", "index")
+    pipeline = builder.build("incremental-index")
+
+    serializer = PipelineSerializer()
+    serialized = serializer.serialize_pipeline(pipeline, format=serialization_format)
+    restored = serializer.deserialize_pipeline(serialized)
+
+    index_step = next(step for step in restored.steps if step.name == "index")
+    assert index_step.dependencies == ["extract"]
+    assert index_step.delta_mode is True
+    assert index_step.base_version_id == "v1"
+    assert index_step.target_version_id == "v2"
+
+
+@pytest.mark.parametrize("serialization_format", ["dict", "json"])
+def test_serialization_omits_runtime_handlers(serialization_format):
+    def handler(data, **config):
+        return data
+
+    builder = PipelineBuilder()
+    builder.add_step("extract", "source", handler=handler, batch_size=10)
+    pipeline = builder.build("handler-pipeline")
+
+    serializer = PipelineSerializer()
+    serialized = serializer.serialize_pipeline(pipeline, format=serialization_format)
+    serialized_data = (
+        json.loads(serialized) if isinstance(serialized, str) else serialized
+    )
+
+    assert serialized_data["steps"][0]["config"] == {"batch_size": 10}
+
+    restored = serializer.deserialize_pipeline(serialized)
+    assert restored.steps[0].handler is None
+    assert restored.steps[0].config == {"batch_size": 10}
+
+
+def test_deserialization_ignores_legacy_stringified_handler():
+    serialized = json.dumps(
+        {
+            "name": "legacy-handler-pipeline",
+            "steps": [
+                {
+                    "name": "extract",
+                    "type": "source",
+                    "config": {
+                        "handler": "<function extract at 0x1234>",
+                        "batch_size": 10,
+                    },
+                    "dependencies": [],
+                }
+            ],
+        }
+    )
+
+    restored = PipelineSerializer().deserialize_pipeline(serialized)
+
+    assert restored.steps[0].handler is None
+    assert restored.steps[0].config == {"batch_size": 10}
+
+
+def test_deserialization_does_not_mutate_caller_owned_dict():
+    payload = {
+        "name": "legacy-handler-pipeline",
+        "steps": [
+            {
+                "name": "extract",
+                "type": "source",
+                "config": {
+                    "handler": "<function extract at 0x1234>",
+                    "batch_size": 10,
+                },
+                "dependencies": [],
+            }
+        ],
+    }
+    snapshot = copy.deepcopy(payload)
+
+    restored = PipelineSerializer().deserialize_pipeline(payload)
+
+    assert payload == snapshot
+    assert "handler" in payload["steps"][0]["config"]
+    assert payload is not snapshot
+    assert restored.steps[0].handler is None
+    assert restored.steps[0].config == {"batch_size": 10}