diff --git a/backend/danswer/connectors/github_files/connector.py b/backend/danswer/connectors/github_files/connector.py
index 0d890923437..7d34e74e5dd 100644
--- a/backend/danswer/connectors/github_files/connector.py
+++ b/backend/danswer/connectors/github_files/connector.py
@@ -1,18 +1,20 @@
-"""GitHub Files connector — indexes files (default: JSON) sitting at a fixed
-depth under a configurable path prefix.
+"""GitHub Files connector — indexes files matching a given extension under
+a configurable path prefix in a repository.
 
-Matches the layout
+Two modes:
 
-    <path_prefix>/<single_dir>/<file><extension>
+- Fixed-depth (default): matches `<path_prefix>/<single_dir>/<file><extension>`
+  — i.e. exactly one folder under the prefix, file directly inside. Default
+  settings target a service-catalog layout:
+      service-catalog/products/<product>/<file>.json
+  Anything deeper or shallower is skipped.
 
-i.e. exactly one folder under the prefix, file directly inside that folder.
-Default settings target a service-catalog layout:
+- Recursive (`recursive=True`): walks every folder under `path_prefix`
+  (the whole repo if the prefix is empty) and matches by extension at any
+  depth. Useful for "index all .md files in the repo" style configurations.
 
-    service-catalog/products/<product>/<file>.json
-
-Anything deeper or shallower is skipped, as are files at intermediate
-directories. The connector reuses the existing GitHub access token credential
-shape, so users don't need to re-enter their PAT.
+The connector reuses the existing GitHub access token credential shape, so
+users don't need to re-enter their PAT.
 """
 import time
 from datetime import datetime
@@ -76,6 +78,7 @@ def __init__(
         path_prefix: str = _DEFAULT_PATH_PREFIX,
         file_extension: str = _DEFAULT_FILE_EXTENSION,
         branch: str = "",
+        recursive: bool = False,
         batch_size: int = INDEX_BATCH_SIZE,
     ) -> None:
         self.repo_owner = repo_owner
@@ -86,6 +89,7 @@ def __init__(
             file_extension if file_extension.startswith(".") else f".{file_extension}"
         ).lower()
         self.branch = branch or ""  # empty -> use repo's default branch
+        self.recursive = recursive
         self.batch_size = batch_size
         self.github_client: Github | None = None
 
@@ -112,7 +116,9 @@ def _resolve_branch(self, repo) -> str:
 
     def _list_matching_paths(self, repo, branch: str) -> list[tuple[str, str]]:
         """Walk the git tree once, returning (path, blob_sha) pairs for files
-        matching `<prefix>/<single_dir>/<file><extension>`."""
+        matching the configured extension. In fixed-depth mode, only files at
+        `<prefix>/<single_dir>/<file><extension>` match; in recursive mode,
+        any file under `<prefix>` (or the repo root) at any depth matches."""
         branch_obj = _retry_on_rate_limit(self.github_client, repo.get_branch, branch)
         head_sha = branch_obj.commit.sha
         tree = _retry_on_rate_limit(
@@ -129,9 +135,10 @@ def _list_matching_paths(self, repo, branch: str) -> list[tuple[str, str]]:
             path = element.path
             if prefix and not path.startswith(prefix + "/"):
                 continue
-            parts = path.split("/")
-            if len(parts) != expected_depth:
-                continue
+            if not self.recursive:
+                parts = path.split("/")
+                if len(parts) != expected_depth:
+                    continue
             if not path.lower().endswith(self.file_extension):
                 continue
             results.append((path, element.sha))
@@ -177,13 +184,20 @@ def _convert_to_document(
         # while unchanged files stay deduped across runs.
         doc_id = f"{html_url}@{sha}"
 
+        # In recursive mode files at different depths can share a filename, so
+        # use the full repo-relative path as the semantic identifier.
+        if self.recursive:
+            semantic_identifier = path
+        else:
+            semantic_identifier = (
+                f"{product_dir}/{filename}" if product_dir else filename
+            )
+
         return Document(
             id=doc_id,
             sections=[Section(link=html_url, text=text)],
             source=DocumentSource.GITHUB_FILES,
-            semantic_identifier=f"{product_dir}/{filename}"
-            if product_dir
-            else filename,
+            semantic_identifier=semantic_identifier,
             doc_updated_at=doc_updated_at,
             metadata={
                 "repo": repo.full_name,
@@ -211,7 +225,7 @@ def _fetch_documents(
             try:
                 commits_iter = repo.get_commits(
                     sha=branch,
-                    path=self.path_prefix or None,
+                    **({"path": self.path_prefix} if self.path_prefix else {}),
                     **({"since": start} if start else {}),
                     **({"until": end} if end else {}),
                 )
@@ -283,6 +297,7 @@ def poll_source(
         path_prefix=os.environ.get("PATH_PREFIX", _DEFAULT_PATH_PREFIX),
         file_extension=os.environ.get("FILE_EXTENSION", _DEFAULT_FILE_EXTENSION),
         branch=os.environ.get("BRANCH", ""),
+        recursive=os.environ.get("RECURSIVE", "").lower() in ("1", "true", "yes"),
     )
     connector.load_credentials(
         {"github_access_token": os.environ["GITHUB_ACCESS_TOKEN"]}
diff --git a/web/src/app/admin/connectors/github-files/page.tsx b/web/src/app/admin/connectors/github-files/page.tsx
index eeea6809413..7adfe8d8dce 100644
--- a/web/src/app/admin/connectors/github-files/page.tsx
+++ b/web/src/app/admin/connectors/github-files/page.tsx
@@ -3,7 +3,10 @@
 import * as Yup from "yup";
 import { useState } from "react";
 import { EditIcon, GithubIcon, TrashIcon } from "@/components/icons/icons";
-import { TextFormField } from "@/components/admin/connectors/Field";
+import {
+  BooleanFormField,
+  TextFormField,
+} from "@/components/admin/connectors/Field";
 import { HealthCheckBanner } from "@/components/health/healthcheck";
 import useSWR, { useSWRConfig } from "swr";
 import { errorHandlingFetcher } from "@/lib/fetcher";
@@ -226,7 +229,11 @@ const Main = () => {
                     const c = ccPairStatus.connector.connector_specific_config;
                     const ext = c.file_extension || ".json";
                     const branch = c.branch ? `@${c.branch}` : "";
-                    return `${c.path_prefix}/<dir>/*${ext}${branch}`;
+                    const root = c.path_prefix || "<repo root>";
+                    const pattern = c.recursive
+                      ? `${root}/**/*${ext}`
+                      : `${root}/<dir>/*${ext}`;
+                    return `${pattern}${branch}`;
                   },
                 },
               ]}
@@ -247,6 +254,9 @@ const Main = () => {
             — i.e. exactly one folder under the prefix, file directly inside.
             Defaults target a{" "}
             <code>service-catalog/products/&lt;product&gt;/*.json</code> layout.
+            Enable <em>Recursive</em> to walk every folder under the prefix
+            (or the whole repo if the prefix is blank) and match by extension
+            at any depth — e.g. <code>*.md</code> across the entire repo.
           </Text>
 
           <ConnectorForm<GithubFilesConfig>
@@ -267,21 +277,29 @@ const Main = () => {
                   label="Path Prefix:"
                   subtext={
                     <>
-                      The folder containing per-product subfolders. Files are
-                      indexed at exactly one level deeper.
+                      The folder to scan. In the default mode, files are
+                      indexed exactly one level deeper (e.g.{" "}
+                      <code>&lt;prefix&gt;/&lt;dir&gt;/*&lt;ext&gt;</code>). In
+                      recursive mode this is the root of the walk; leave blank
+                      to scan the whole repository.
                     </>
                   }
                 />
                 <TextFormField
                   name="file_extension"
                   label="File Extension:"
-                  subtext="e.g. .json — only files with this extension at the matching depth are indexed."
+                  subtext="e.g. .md — only files with this extension are indexed."
                 />
                 <TextFormField
                   name="branch"
                   label="Branch (optional):"
                   subtext="Leave blank to use the repository's default branch."
                 />
+                <BooleanFormField
+                  name="recursive"
+                  label="Recursive"
+                  subtext="Walk all subfolders under the path prefix and match files by extension at any depth. Leave off for the fixed depth (<prefix>/<dir>/<file>) layout."
+                />
               </>
             }
             validationSchema={Yup.object().shape({
@@ -291,13 +309,23 @@ const Main = () => {
               repo_name: Yup.string().required(
                 "Please enter the name of the repository"
               ),
-              path_prefix: Yup.string().required(
-                "Please enter the path prefix to scan"
-              ),
+              path_prefix: Yup.string()
+                .defined()
+                .test(
+                  "required-unless-recursive",
+                  "Please enter the path prefix to scan",
+                  function (value) {
+                    return (
+                      Boolean(this.parent.recursive) ||
+                      (typeof value === "string" && value.length > 0)
+                    );
+                  }
+                ),
               file_extension: Yup.string().required(
                 "Please enter the file extension to filter on"
               ),
               branch: Yup.string(),
+              recursive: Yup.boolean(),
             })}
             initialValues={{
               repo_owner: "",
@@ -305,6 +333,7 @@ const Main = () => {
               path_prefix: "service-catalog/products",
               file_extension: ".json",
               branch: "",
+              recursive: false,
             }}
             refreshFreq={10 * 60}
             credentialId={githubCredential.id}
diff --git a/web/src/lib/types.ts b/web/src/lib/types.ts
index dd5adb9685c..ad76e1f2541 100644
--- a/web/src/lib/types.ts
+++ b/web/src/lib/types.ts
@@ -125,6 +125,7 @@ export interface GithubFilesConfig {
   path_prefix: string;
   file_extension: string;
   branch?: string;
+  recursive?: boolean;
 }
 
 export interface GitlabConfig {