diff --git a/src/utils.cc b/src/utils.cc
index 19cc0c28..a0534504 100644
--- a/src/utils.cc
+++ b/src/utils.cc
@@ -53,6 +53,10 @@ auto handle_json_entry(
                          return prefix == canonical ||
                                 path_starts_with(canonical, prefix);
                        })) {
+        if (std::filesystem::is_empty(canonical)) {
+          continue;
+        }
+
         // TODO: Print a verbose message for what is getting parsed
         result.emplace_back(canonical,
                             sourcemeta::jsontoolkit::from_file(canonical));
@@ -75,6 +79,10 @@ auto handle_json_entry(
                        return prefix == canonical ||
                               path_starts_with(canonical, prefix);
                      })) {
+      if (std::filesystem::is_empty(canonical)) {
+        return;
+      }
+
       // TODO: Print a verbose message for what is getting parsed
       result.emplace_back(canonical,
                           sourcemeta::jsontoolkit::from_file(canonical));
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index ae3945a4..252980ee 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -38,6 +38,7 @@ add_jsonschema_test_unix(validate_fail_no_schema)
 add_jsonschema_test_unix(validate_fail_no_instance)
 add_jsonschema_test_unix(validate_non_supported)
 add_jsonschema_test_unix(bundle_non_remote)
+add_jsonschema_test_unix(bundle_into_resolve_directory)
 add_jsonschema_test_unix(bundle_remote_single_schema)
 add_jsonschema_test_unix(bundle_remote_no_http)
 add_jsonschema_test_unix(bundle_remote_directory)
diff --git a/test/bundle_into_resolve_directory.sh b/test/bundle_into_resolve_directory.sh
new file mode 100755
index 00000000..087d80fe
--- /dev/null
+++ b/test/bundle_into_resolve_directory.sh
@@ -0,0 +1,44 @@
+#!/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",
+  "$id": "https://example.com",
+  "$ref": "nested"
+}
+EOF
+
+mkdir "$TMP/schemas"
+cat << 'EOF' > "$TMP/schemas/remote.json"
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://example.com/nested",
+  "type": "string"
+}
+EOF
+
+"$1" bundle "$TMP/schema.json" --resolve "$TMP/schemas" > "$TMP/schemas/result.json"
+
+cat << 'EOF' > "$TMP/expected.json"
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://example.com",
+  "$ref": "nested",
+  "$defs": {
+    "https://example.com/nested": {
+      "$schema": "https://json-schema.org/draft/2020-12/schema",
+      "$id": "https://example.com/nested",
+      "type": "string"
+    }
+  }
+}
+EOF
+
+diff "$TMP/schemas/result.json" "$TMP/expected.json"