diff --git a/src/input.h b/src/input.h
index fd5f3de5..3957e487 100644
--- a/src/input.h
+++ b/src/input.h
@@ -309,6 +309,8 @@ inline auto for_each_json(const std::vector<std::string_view> &arguments,
                           ? configuration.value().absolute_path
                           : current_path,
                       blacklist, extensions, result, options);
+    std::sort(result.begin(), result.end(),
+              [](const auto &left, const auto &right) { return left < right; });
   } else {
     std::unordered_set<std::string> seen_configurations;
     for (const auto &entry : arguments) {
@@ -328,13 +330,14 @@ inline auto for_each_json(const std::vector<std::string_view> &arguments,
 
     const auto extensions{parse_extensions(options, std::nullopt)};
     for (const auto &entry : arguments) {
+      const auto before{result.size()};
       handle_json_entry(entry, blacklist, extensions, result, options);
+      std::sort(
+          result.begin() + static_cast<std::ptrdiff_t>(before), result.end(),
+          [](const auto &left, const auto &right) { return left < right; });
     }
   }
 
-  std::sort(result.begin(), result.end(),
-            [](const auto &left, const auto &right) { return left < right; });
-
   return result;
 }
 
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index a145842f..0c340c4a 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -110,6 +110,7 @@ add_jsonschema_test_unix(validate/fail_resolve_invalid_id)
 add_jsonschema_test_unix(validate/fail_resolve_invalid_recursive_ref)
 add_jsonschema_test_unix(validate/fail_resolve_missing_core_vocabulary)
 add_jsonschema_test_unix(validate/fail_resolve_relative_metaschema)
+add_jsonschema_test_unix(validate/pass_resolve_custom_metaschema_ordering)
 add_jsonschema_test_unix(validate/pass_jsonl_bigint)
 add_jsonschema_test_unix(validate/fail_trace)
 add_jsonschema_test_unix(validate/fail_trace_fast)
diff --git a/test/validate/pass_resolve_custom_metaschema_ordering.sh b/test/validate/pass_resolve_custom_metaschema_ordering.sh
new file mode 100755
index 00000000..2add0be8
--- /dev/null
+++ b/test/validate/pass_resolve_custom_metaschema_ordering.sh
@@ -0,0 +1,56 @@
+#!/bin/sh
+
+set -o errexit
+set -o nounset
+
+TMP="$(mktemp -d)"
+clean() { rm -rf "$TMP"; }
+trap clean EXIT
+
+cat << 'EOF' > "$TMP/schema.json"
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$ref": "https://example.com/my-schema"
+}
+EOF
+
+cat << 'EOF' > "$TMP/zz-meta.json"
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://example.com/my-meta",
+  "$vocabulary": {
+    "https://json-schema.org/draft/2020-12/vocab/core": true,
+    "https://json-schema.org/draft/2020-12/vocab/applicator": true,
+    "https://json-schema.org/draft/2020-12/vocab/validation": true
+  }
+}
+EOF
+
+cat << 'EOF' > "$TMP/aa-schema.json"
+{
+  "$schema": "https://example.com/my-meta",
+  "$id": "https://example.com/my-schema",
+  "type": "string"
+}
+EOF
+
+cat << 'EOF' > "$TMP/instance.json"
+"hello"
+EOF
+
+"$1" validate "$TMP/schema.json" "$TMP/instance.json" \
+  --resolve "$TMP/zz-meta.json" \
+  --resolve "$TMP/aa-schema.json" --debug 2>"$TMP/stderr.txt"
+
+cat << EOF > "$TMP/expected.txt"
+debug: Detecting schema resources from file: $(realpath "$TMP")/zz-meta.json
+debug: Importing schema into the resolution context: file://$(realpath "$TMP")/zz-meta.json
+debug: Importing schema into the resolution context: https://example.com/my-meta
+debug: Detecting schema resources from file: $(realpath "$TMP")/aa-schema.json
+debug: Importing schema into the resolution context: file://$(realpath "$TMP")/aa-schema.json
+debug: Importing schema into the resolution context: https://example.com/my-schema
+ok: $(realpath "$TMP")/instance.json
+  matches $(realpath "$TMP")/schema.json
+EOF
+
+diff "$TMP/stderr.txt" "$TMP/expected.txt"