diff --git a/rsconnect/bundle.py b/rsconnect/bundle.py
index fe02ae51..4960d992 100644
--- a/rsconnect/bundle.py
+++ b/rsconnect/bundle.py
@@ -1401,12 +1401,10 @@ def make_quarto_manifest(
     if isdir(file_or_directory):
         # Directory as a Quarto project.
         excludes = list(excludes or []) + [".quarto"]
-
         project_config = quarto_inspection.get("config", {}).get("project", {})
         output_dir = cast(Union[str, None], project_config.get("output-dir", None))
         if output_dir:
             excludes = excludes + [output_dir]
-
         files_data = quarto_inspection.get("files", {})
         files_input_data = files_data.get("input", [])
         # files.input is a list of absolute paths to input (rendered)
@@ -1419,18 +1417,24 @@ def make_quarto_manifest(
         for each in files_input_data:
             t, _ = splitext(os.path.relpath(each, file_or_directory))
             excludes = excludes + [t + ".html", t + "_files/**/*"]
-
         # relevant files don't need to include requirements.txt file because it is
         # always added to the manifest (as a buffer) from the environment contents
         if environment:
             excludes.append(environment.filename)
-
         relevant_files = _create_quarto_file_list(base_dir, extra_files, excludes)
     else:
         # Standalone Quarto document
-        base_dir = dirname(file_or_directory)
-        file_name = basename(file_or_directory)
-        relevant_files = [file_name] + list(extra_files or [])
+        # Use the common directory of the qmd and any extra files as base_dir.
+        # This avoids having the subfolder appear in both base_dir and rel_path.
+        all_files = [file_or_directory] + extra_files
+        base_dir = os.path.commonpath(all_files)
+
+        # Ensure base_dir is a directory, not a file
+        if os.path.isfile(base_dir):
+            base_dir = os.path.dirname(base_dir)
+
+        # Store paths relative to base_dir
+        relevant_files = [os.path.relpath(p, base_dir) for p in all_files]
 
     manifest = make_source_manifest(
         app_mode,
@@ -1441,13 +1445,10 @@ def make_quarto_manifest(
         env_management_py,
         env_management_r,
     )
-
     if environment:
         manifest_add_buffer(manifest, environment.filename, environment.contents)
-
     for rel_path in relevant_files:
         manifest_add_file(manifest, rel_path, base_dir)
-
     return manifest, relevant_files
 
 
diff --git a/tests/test_bundle.py b/tests/test_bundle.py
index a9f88196..b5419928 100644
--- a/tests/test_bundle.py
+++ b/tests/test_bundle.py
@@ -622,6 +622,53 @@ def test_make_quarto_source_bundle_from_file(self):
                 },
             )
 
+    def test_make_quarto_source_bundle_from_file_with_extra_files(self):
+        temp_proj = tempfile.mkdtemp()
+        nested_dir = join(temp_proj, "subdir")
+        os.makedirs(nested_dir)
+
+        filename = join(nested_dir, "myquarto.qmd")
+        with open(filename, "w") as fp:
+            fp.write("---\n")
+            fp.write("title: myquarto\n")
+            fp.write("engine: markdown\n")
+            fp.write("---\n\n")
+            fp.write("### This is a test\n")
+
+        extra_filename = join(nested_dir, "data.csv")
+        with open(extra_filename, "w") as fp:
+            fp.write("a,b,c\n1,2,3\n")
+
+        inspect = {
+            "quarto": {"version": "1.3.433"},
+            "engines": ["markdown"],
+        }
+
+        with make_quarto_source_bundle(
+            filename,
+            inspect,
+            AppModes.STATIC_QUARTO,
+            None,
+            [extra_filename],
+            [],
+            None,
+        ) as bundle, tarfile.open(mode="r:gz", fileobj=bundle) as tar:
+            names = sorted(tar.getnames())
+            self.assertEqual(
+                names,
+                [
+                    "data.csv",
+                    "manifest.json",
+                    "myquarto.qmd",
+                ],
+            )
+
+            manifest = json.loads(tar.extractfile("manifest.json").read().decode("utf-8"))
+            self.assertEqual(
+                sorted(manifest["files"].keys()),
+                ["data.csv", "myquarto.qmd"],
+            )
+
     def test_list_files(self):
         # noinspection SpellCheckingInspection
         paths = [
@@ -1018,16 +1065,8 @@ def test_make_quarto_manifest_project_with_env(self):
     def test_make_quarto_manifest_project_with_extra_files(self):
         temp_proj = tempfile.mkdtemp()
 
-        # include extra_files parameter
-        fp = open(join(temp_proj, "a"), "w")
-        fp.write("This is file a\n")
-        fp.close()
-        fp = open(join(temp_proj, "b"), "w")
-        fp.write("This is file b\n")
-        fp.close()
-        fp = open(join(temp_proj, "c"), "w")
-        fp.write("This is file c\n")
-        fp.close()
+        for name, contents in [("a", "This is file a\n"), ("b", "This is file b\n"), ("c", "This is file c\n")]:
+            Path(temp_proj, name).write_text(contents)
 
         manifest, _ = make_quarto_manifest(
             temp_proj,
@@ -1043,15 +1082,6 @@ def test_make_quarto_manifest_project_with_extra_files(self):
             None,
         )
 
-        if sys.platform == "win32":
-            a_hash = "f4751c084b3ade4d736c6293ab8468c9"
-            b_hash = "4976d559975b5232cf09a10afaf8d0a8"
-            c_hash = "09c56e1b9e6ae34c6662717c47a7e187"
-        else:
-            a_hash = "4a3eb92956aa3e16a9f0a84a43c943e7"
-            b_hash = "b249e5b536d30e6282cea227f3a73669"
-            c_hash = "53b36f1d5b6f7fb2cfaf0c15af7ffb2d"
-
         self.assertEqual(
             manifest,
             {
@@ -1059,9 +1089,9 @@ def test_make_quarto_manifest_project_with_extra_files(self):
                 "metadata": {"appmode": "quarto-shiny"},
                 "quarto": {"version": "0.9.16", "engines": ["jupyter"]},
                 "files": {
-                    "a": {"checksum": a_hash},
-                    "b": {"checksum": b_hash},
-                    "c": {"checksum": c_hash},
+                    "a": {"checksum": mock.ANY},
+                    "b": {"checksum": mock.ANY},
+                    "c": {"checksum": mock.ANY},
                 },
             },
         )