diff --git a/dandi/bids_validator_deno/_validator.py b/dandi/bids_validator_deno/_validator.py
index d97f953db..7e28bb7cc 100644
--- a/dandi/bids_validator_deno/_validator.py
+++ b/dandi/bids_validator_deno/_validator.py
@@ -12,8 +12,10 @@
 from packaging.version import parse as parse_ver_str
 from pydantic import DirectoryPath, validate_call
 
+from dandi.consts import dandiset_metadata_file
 from dandi.utils import find_parent_directory_containing
 from dandi.validate_types import (
+    ORIGIN_VALIDATION_DANDI_LAYOUT,
     Origin,
     OriginType,
     Scope,
@@ -361,20 +363,45 @@ def _harmonize(
         # The absolute path to the file or directory that the issue is related to
         issue_path = _get_path(issue, ds_path)
 
-        results.append(
-            ValidationResult(
-                id=f"BIDS.{issue.code}",
-                origin=origin,
-                scope=_get_scope(issue_path),
-                # Store only the issue, not entire bv_result with more context
-                origin_result=issue,
-                severity=_SEVERITY_MAP[severity] if severity else None,
+        validation_result = ValidationResult(
+            id=f"BIDS.{issue.code}",
+            origin=origin,
+            scope=_get_scope(issue_path),
+            # Store only the issue, not entire bv_result with more context
+            origin_result=issue,
+            severity=_SEVERITY_MAP[severity] if severity else None,
+            dandiset_path=dandiset_path,
+            dataset_path=ds_path,
+            message=_get_msg(issue, code_messages),
+            path=issue_path,
+        )
+        results.append(validation_result)
+
+        # If the error is about the dandiset metadata file, add a HINT
+        # suggesting to add it to .bidsignore
+        is_dandiset_yaml_error = (
+            issue_path is not None
+            and issue_path.relative_to(ds_path).as_posix() == dandiset_metadata_file
+        )
+        if is_dandiset_yaml_error:
+            hint = ValidationResult(
+                id="DANDI.BIDSIGNORE_DANDISET_YAML",
+                origin=ORIGIN_VALIDATION_DANDI_LAYOUT,
+                scope=Scope.DATASET,
+                origin_result=validation_result,
+                severity=Severity.HINT,
                 dandiset_path=dandiset_path,
                 dataset_path=ds_path,
-                message=_get_msg(issue, code_messages),
                 path=issue_path,
+                message=(
+                    f"Consider creating or updating a `.bidsignore` file "
+                    f"in the root of your BIDS dataset to ignore "
+                    f"`{dandiset_metadata_file}`. "
+                    f"Add the following line to `.bidsignore`:\n"
+                    f"{dandiset_metadata_file}"
+                ),
             )
-        )
+            results.append(hint)
 
     return results
 
diff --git a/dandi/tests/test_validate.py b/dandi/tests/test_validate.py
index 5b240eff8..703de8730 100644
--- a/dandi/tests/test_validate.py
+++ b/dandi/tests/test_validate.py
@@ -114,11 +114,30 @@ def mock_bids_validate(*args: Any, **kwargs: Any) -> list[ValidationResult]:
     assert err.dataset_path is not None
     assert err.path.relative_to(err.dataset_path).as_posix() == dandiset_metadata_file
 
+    # The error message should be the original BIDS error, not modified
     assert err.message is not None
-    assert err.message.startswith(
-        f"The dandiset metadata file, `{dandiset_metadata_file}`, is not a part of "
-        f"BIDS specification."
+    # We just check that it's about dandiset.yaml, not checking exact message
+    # since it comes from BIDS validator
+
+    # Check that there is also a HINT about .bidsignore
+    validation_hints = [
+        r
+        for r in validation_results
+        if r.severity is not None and r.severity == Severity.HINT
+    ]
+
+    # Assert that there is at least one hint
+    assert len(validation_hints) >= 1
+
+    # Find the hint about .bidsignore for dandiset.yaml
+    bidsignore_hint = next(
+        (h for h in validation_hints if h.id == "DANDI.BIDSIGNORE_DANDISET_YAML"),
+        None,
     )
+    assert bidsignore_hint is not None
+    assert bidsignore_hint.message is not None
+    assert ".bidsignore" in bidsignore_hint.message
+    assert dandiset_metadata_file in bidsignore_hint.message
 
 
 def test_validate_bids_onefile(bids_error_examples: Path, tmp_path: Path) -> None:
diff --git a/dandi/validate.py b/dandi/validate.py
index e67dfb383..3b4dae26f 100644
--- a/dandi/validate.py
+++ b/dandi/validate.py
@@ -186,22 +186,6 @@ def validate(
             ):
                 r_id = id(r)
                 if r_id not in df_result_ids:
-                    # If the error is about the dandiset metadata file, modify
-                    # the message in the validation to give the context of DANDI
-                    if (
-                        r.path is not None
-                        and r.dataset_path is not None
-                        and r.path.relative_to(r.dataset_path).as_posix()
-                        == dandiset_metadata_file
-                    ):
-                        r.message = (
-                            f"The dandiset metadata file, `{dandiset_metadata_file}`, "
-                            f"is not a part of BIDS specification. Please include a "
-                            f"`.bidsignore` file with specification to ignore the "
-                            f"metadata file in your dataset. For more details, see "
-                            f"https://github.com/bids-standard/bids-specification/"
-                            f"issues/131#issuecomment-461060166."
-                        )
                     df_results.append(r)
                     df_result_ids.add(r_id)
                     yield r