diff --git a/localstack/services/s3/presigned_url.py b/localstack/services/s3/presigned_url.py
index 9d9af903d808e..260961388926d 100644
--- a/localstack/services/s3/presigned_url.py
+++ b/localstack/services/s3/presigned_url.py
@@ -64,20 +64,7 @@
 # headers to blacklist from request_dict.signed_headers
 BLACKLISTED_HEADERS = ["X-Amz-Security-Token"]
 
-# query params overrides for multipart upload and node sdk
-# TODO: this will depends on query/post v2/v4. Manage independently
-ALLOWED_QUERY_PARAMS = [
-    "x-id",
-    "x-amz-user-agent",
-    "x-amz-content-sha256",
-    "versionid",
-    "uploadid",
-    "partnumber",
-]
-
 IGNORED_SIGV4_HEADERS = [
-    "x-id",
-    "x-amz-user-agent",
     "x-amz-content-sha256",
 ]
 
@@ -578,11 +565,10 @@ def _get_signed_headers_and_filtered_query_string(self) -> Tuple[Dict[str, str],
         not_signed_headers = []
         for header, value in headers.items():
             header_low = header.lower()
-            if header_low.startswith("x-amz-"):
+            if header_low.startswith("x-amz-") and header_low not in signed_headers.lower():
                 if header_low in IGNORED_SIGV4_HEADERS:
                     continue
-                if header_low not in signed_headers.lower():
-                    not_signed_headers.append(header_low)
+                not_signed_headers.append(header_low)
             if header_low in signed_headers:
                 signature_headers[header_low] = value
 
diff --git a/tests/aws/services/s3/test_s3.py b/tests/aws/services/s3/test_s3.py
index 3ef714a1b2e9e..de59aadc50a38 100644
--- a/tests/aws/services/s3/test_s3.py
+++ b/tests/aws/services/s3/test_s3.py
@@ -10,6 +10,7 @@
 import shutil
 import tempfile
 import time
+from importlib.util import find_spec
 from io import BytesIO
 from operator import itemgetter
 from typing import TYPE_CHECKING
@@ -6546,7 +6547,7 @@ def test_pre_signed_url_forward_slash_bucket(
         "signature_version",
         ["s3", "s3v4"],
     )
-    @markers.aws.unknown
+    @markers.aws.validated
     def test_s3_presign_url_encoding(
         self, aws_client, s3_bucket, signature_version, patch_s3_skip_signature_validation_false
     ):
@@ -6568,6 +6569,86 @@ def test_s3_presign_url_encoding(
         assert req.ok
         assert req.content == b"123"
 
+    @markers.aws.validated
+    def test_s3_ignored_special_headers(
+        self,
+        s3_bucket,
+        patch_s3_skip_signature_validation_false,
+        monkeypatch,
+    ):
+        # if the crt.auth is not available, not need to patch as it will use it by default
+        if find_spec("botocore.crt.auth"):
+            # the CRT client does not allow us to pass a protected header, it will trigger an exception, so we need
+            # to patch the Signer selection to the Python implementation which does not have this check
+            from botocore.auth import AUTH_TYPE_MAPS, S3SigV4QueryAuth
+
+            monkeypatch.setitem(AUTH_TYPE_MAPS, "s3v4-query", S3SigV4QueryAuth)
+
+        key = "my-key"
+        presigned_client = _s3_client_custom_config(
+            Config(signature_version="s3v4", s3={"payload_signing_enabled": True}),
+            endpoint_url=_endpoint_url(),
+        )
+
+        def add_content_sha_header(request, **kwargs):
+            request.headers["x-amz-content-sha256"] = "UNSIGNED-PAYLOAD"
+
+        presigned_client.meta.events.register(
+            "before-sign.s3.PutObject",
+            handler=add_content_sha_header,
+        )
+        try:
+            url = presigned_client.generate_presigned_url(
+                "put_object", Params={"Bucket": s3_bucket, "Key": key}
+            )
+            assert "x-amz-content-sha256" in url
+            # somehow, it's possible to add "x-amz-content-sha256" to signed headers, the AWS Go SDK does it
+            resp = requests.put(
+                url,
+                data="something",
+                verify=False,
+                headers={"x-amz-content-sha256": "UNSIGNED-PAYLOAD"},
+            )
+            assert resp.ok
+
+            # if signed but not provided, AWS will raise an exception
+            resp = requests.put(url, data="something", verify=False)
+            assert resp.status_code == 403
+
+        finally:
+            presigned_client.meta.events.unregister(
+                "before-sign.s3.PutObject",
+                add_content_sha_header,
+            )
+
+        # recreate the request, without the signed header
+        url = presigned_client.generate_presigned_url(
+            "put_object", Params={"Bucket": s3_bucket, "Key": key}
+        )
+        assert "x-amz-content-sha256" not in url
+
+        # assert that if provided and not signed, AWS will ignore it even if it starts with `x-amz`
+        resp = requests.put(
+            url,
+            data="something",
+            verify=False,
+            headers={"x-amz-content-sha256": "UNSIGNED-PAYLOAD"},
+        )
+        assert resp.ok
+
+        # assert that x-amz-user-agent is not ignored, it must be set in SignedHeaders
+        resp = requests.put(
+            url, data="something", verify=False, headers={"x-amz-user-agent": "test"}
+        )
+        assert resp.status_code == 403
+
+        # X-Amz-Signature needs to be the last query string parameter: insert x-id before like the Go SDK
+        index = url.find("&X-Amz-Signature")
+        rewritten_url = url[:index] + "&x-id=PutObject" + url[index:]
+        # however, the x-id query string parameter is not ignored
+        resp = requests.put(rewritten_url, data="something", verify=False)
+        assert resp.status_code == 403
+
 
 class TestS3DeepArchive:
     """