diff --git a/pr_agent/git_providers/github_provider.py b/pr_agent/git_providers/github_provider.py
index feee84a0..3a6264eb 100644
--- a/pr_agent/git_providers/github_provider.py
+++ b/pr_agent/git_providers/github_provider.py
@@ -10,6 +10,7 @@ from datetime import datetime
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
+from github.Issue import Issue
 from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
 from starlette_context import context
@@ -42,6 +43,7 @@ class GithubProvider(GitProvider):
         self.repo = None
         self.pr_num = None
         self.pr = None
+        self.issue_main = None
         self.github_user_id = None
         self.diff_files = None
         self.git_files = None
@@ -51,9 +53,29 @@ class GithubProvider(GitProvider):
             self.pr_commits = list(self.pr.get_commits())
             self.last_commit_id = self.pr_commits[-1]
             self.pr_url = self.get_pr_url() # pr_url for github actions can be as api.github.com, so we need to get the url from the pr object
-        else:
+        elif pr_url and 'issue' in pr_url: #url is an issue
+            self.issue_main = self._get_issue_handle(pr_url)
+        else: #Instantiated the provider without a PR / Issue
             self.pr_commits = None
 
+    def _get_issue_handle(self, issue_url) -> Optional[Issue]:
+        repo_name, issue_number = self._parse_issue_url(issue_url)
+        if not repo_name or not issue_number:
+            get_logger().error(f"Given url: {issue_url} is not a valid issue.")
+            return None
+        # else: Check if can get a valid Repo handle:
+        try:
+            repo_obj = self.github_client.get_repo(repo_name)
+            if not repo_obj:
+                get_logger().error(f"Given url: {issue_url}, belonging to owner/repo: {repo_name} does "
+                                   f"not have a valid repository: {self.get_git_repo_url(issue_url)}")
+                return None
+            # else: Valid repo handle:
+            return repo_obj.get_issue(issue_number)
+        except Exception as e:
+            get_logger().exception(f"Failed to get an issue object for issue: {issue_url}, belonging to owner/repo: {repo_name}")
+            return None
+
     def get_incremental_commits(self, incremental=IncrementalPR(False)):
         self.incremental = incremental
         if self.incremental.is_incremental:
@@ -344,10 +366,19 @@ class GithubProvider(GitProvider):
         self.publish_persistent_comment_full(pr_comment, initial_header, update_header, name, final_update_message)
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        if not self.pr and not self.issue_main:
+            get_logger().error("Cannot publish a comment if missing PR/Issue context")
+            return None
+
         if is_temporary and not get_settings().config.publish_output_progress:
             get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
             return None
         pr_comment = self.limit_output_characters(pr_comment, self.max_comment_chars)
+
+        # In case this is an issue, can publish the comment on the issue.
+        if self.issue_main:
+            return self.issue_main.create_comment(pr_comment)
+
         response = self.pr.create_issue_comment(pr_comment)
         if hasattr(response, "user") and hasattr(response.user, "login"):
             self.github_user_id = response.user.login
@@ -731,11 +762,11 @@ class GithubProvider(GitProvider):
     def _parse_issue_url(self, issue_url: str) -> Tuple[str, int]:
         parsed_url = urlparse(issue_url)
 
-        if 'github.com' not in parsed_url.netloc:
-            raise ValueError("The provided URL is not a valid GitHub URL")
+        if parsed_url.path.startswith('/api/v3'): #Check if came from github app
+            parsed_url = urlparse(issue_url.replace("/api/v3", ""))
 
         path_parts = parsed_url.path.strip('/').split('/')
-        if 'api.github.com' in parsed_url.netloc:
+        if 'api.github.com' in parsed_url.netloc or '/api/v3' in issue_url: #Check if came from github app
             if len(path_parts) < 5 or path_parts[3] != 'issues':
                 raise ValueError("The provided URL does not appear to be a GitHub ISSUE URL")
             repo_name = '/'.join(path_parts[1:3])
diff --git a/pr_agent/tools/pr_help_docs.py b/pr_agent/tools/pr_help_docs.py
index 5695065a..ddd42509 100644
--- a/pr_agent/tools/pr_help_docs.py
+++ b/pr_agent/tools/pr_help_docs.py
@@ -101,6 +101,7 @@ def aggregate_documentation_files_for_prompt_contents(base_path: str, doc_files:
 
 def format_markdown_q_and_a_response(question_str: str, response_str: str, relevant_sections: List[Dict[str, str]],
                                      supported_suffixes: List[str], base_url_prefix: str, base_url_suffix: str="") -> str:
+    base_url_prefix = base_url_prefix.strip('/') #Sanitize base_url_prefix
     answer_str = ""
     answer_str += f"### Question: \n{question_str}\n\n"
     answer_str += f"### Answer:\n{response_str.strip()}\n\n"
@@ -114,9 +115,9 @@ def format_markdown_q_and_a_response(question_str: str, response_str: str, relev
         if str(section['relevant_section_header_string']).strip():
             markdown_header = format_markdown_header(section['relevant_section_header_string'])
             if base_url_prefix:
-                answer_str += f"> - {base_url_prefix}{file}{base_url_suffix}#{markdown_header}\n"
+                answer_str += f"> - {base_url_prefix}/{file}{base_url_suffix}#{markdown_header}\n"
         else:
-            answer_str += f"> - {base_url_prefix}{file}{base_url_suffix}\n"
+            answer_str += f"> - {base_url_prefix}/{file}{base_url_suffix}\n"
     return answer_str
 
 def format_markdown_header(header: str) -> str: