diff --git a/.changelog/5660.fixed b/.changelog/5660.fixed
new file mode 100644
index 0000000000..335362d6c1
--- /dev/null
+++ b/.changelog/5660.fixed
@@ -0,0 +1 @@
+`opentelemetry-sdk`: fix overriding of the service.instance.id which has been populated from the user provided values through the resource detectors
diff --git a/opentelemetry-sdk/src/opentelemetry/sdk/resources/__init__.py b/opentelemetry-sdk/src/opentelemetry/sdk/resources/__init__.py
index 36be319f71..1d9a8e62b8 100644
--- a/opentelemetry-sdk/src/opentelemetry/sdk/resources/__init__.py
+++ b/opentelemetry-sdk/src/opentelemetry/sdk/resources/__init__.py
@@ -545,16 +545,20 @@ def _build_resource_detectors() -> list["ResourceDetector"]:
     Fast path: if no extra detectors are configured, returns only the two
     built-in detectors without scanning entry_points.
 
-    "service_instance" (ServiceInstanceIdResourceDetector) and "otel"
-    (OTELResourceDetector) are always appended as defaults. "otel" is last so
-    that OTEL_RESOURCE_ATTRIBUTES and OTEL_SERVICE_NAME take highest merge
-    priority, but an explicit position in OTEL_EXPERIMENTAL_RESOURCE_DETECTORS
+    "service_instance" (ServiceInstanceIdResourceDetector) is prepended. "otel"
+    (OTELResourceDetector) is last so that OTEL_RESOURCE_ATTRIBUTES and
+    OTEL_SERVICE_NAME take highest merge priority, but an explicit position in OTEL_EXPERIMENTAL_RESOURCE_DETECTORS
     is respected for either name.
     """
     detector_names: list[str] = list(
         dict.fromkeys(
-            [name.strip() for name in environ.get(OTEL_EXPERIMENTAL_RESOURCE_DETECTORS, "").split(",") if name.strip()]
-            + ["service_instance", "otel"]
+            ["service_instance"]
+            + [
+                name.strip()
+                for name in environ.get(OTEL_EXPERIMENTAL_RESOURCE_DETECTORS, "").split(",")
+                if name.strip()
+            ]
+            + ["otel"]
         )
     )
 
diff --git a/opentelemetry-sdk/tests/resources/test_resources.py b/opentelemetry-sdk/tests/resources/test_resources.py
index eec1cdcc93..2666351a50 100644
--- a/opentelemetry-sdk/tests/resources/test_resources.py
+++ b/opentelemetry-sdk/tests/resources/test_resources.py
@@ -1044,6 +1044,42 @@ def tearDown(self) -> None:
     def test_is_process_dependent(self):
         self.assertTrue(ServiceInstanceIdResourceDetector().is_process_dependent())
 
+    @patch.dict(environ, {}, clear=True)
+    def test_service_instance_detector_sets_id_without_custom_detector(self):
+        resource = Resource.create()
+
+        self.assertEqual(uuid.UUID(resource.attributes[SERVICE_INSTANCE_ID]).version, 4)
+
+    @patch.dict(
+        environ,
+        {OTEL_EXPERIMENTAL_RESOURCE_DETECTORS: "mock"},
+        clear=True,
+    )
+    def test_configured_detector_overrides_service_instance_id(self):
+        custom_detector = Mock(spec=ResourceDetector)
+        custom_detector.detect.return_value = Resource(
+            {
+                SERVICE_INSTANCE_ID: "configured-instance-id",
+                "custom.detector": "value",
+            }
+        )
+        entry_point = Mock(**{"load.return_value": Mock(return_value=custom_detector)})
+
+        def side_effect(*args, **kwargs):
+            if kwargs.get("name") == "mock":
+                return [entry_point]
+            return real_entry_points(*args, **kwargs)
+
+        with patch(
+            "opentelemetry.util._importlib_metadata.entry_points",
+            side_effect=side_effect,
+        ):
+            resource = Resource.create()
+
+        custom_detector.detect.assert_called_once()
+        self.assertEqual(resource.attributes[SERVICE_INSTANCE_ID], "configured-instance-id")
+        self.assertEqual(resource.attributes["custom.detector"], "value")
+
     def test_detect_value_is_valid_uuid4(self):
         _resources_module._service_instance_id = None
         _resources_module._service_instance_id_pid = None