diff --git a/main.go b/main.go
index 8cde844..fd99832 100644
--- a/main.go
+++ b/main.go
@@ -1,5 +1,6 @@
 /*
-Copyright 2017, 2020 Vector Creations Ltd
+Copyright 2017 Vector Creations Ltd
+Copyright 2020 The Matrix.org Foundation C.I.C.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -48,7 +49,10 @@ type config struct {
 	// A GitHub personal access token, to create a GitHub issue for each report.
 	GithubToken string `yaml:"github_token"`
 
-	GithubProjectMappings       map[string]string `yaml:"github_project_mappings"`
+	// Mappings from app name (as submitted in the API) to github repo for issue reporting.
+	GithubProjectMappings map[string]string `yaml:"github_project_mappings"`
+	// Mappings from app name (as submitted in the API) to github repo as to which the issues pertain.
+	// Not needed if the issues are reported to the main repo as github will complete the ambiguous references correctly.
 	AutocompleteProjectMappings map[string]string `yaml:"autocomplete_project_mappings"`
 
 	SlackWebhookURL string `yaml:"slack_webhook_url"`
diff --git a/submit.go b/submit.go
index a31aecb..52825ac 100644
--- a/submit.go
+++ b/submit.go
@@ -1,5 +1,6 @@
 /*
-Copyright 2017, 2020 Vector Creations Ltd
+Copyright 2017 Vector Creations Ltd
+Copyright 2020 The Matrix.org Foundation C.I.C.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -120,7 +121,12 @@ type submitResponse struct {
 }
 
 // regex to catch and substitute ambiguous issue references with explicit ones to the actual repo they are in
-var ambiguousIssueRegex = regexp.MustCompile(`[\s,.](#\d+)`)
+var ambiguousIssueRegex = regexp.MustCompile(`(^|[([{\s])(#\d+)([^\w]|$)`)
+
+func replaceAmbiguousIssueReferences(ownerRepo, text string) string {
+	t := ambiguousIssueRegex.ReplaceAllString(text, fmt.Sprintf("${1}%s$2$3", ownerRepo))
+	return t
+}
 
 func (s *submitServer) ServeHTTP(w http.ResponseWriter, req *http.Request) {
 	// if we attempt to return a response without reading the request body,
@@ -168,7 +174,7 @@ func (s *submitServer) ServeHTTP(w http.ResponseWriter, req *http.Request) {
 	}
 
 	if s.autocompleteProjectMappings[p.AppName] != "" {
-		p.UserText = ambiguousIssueRegex.ReplaceAllString(p.UserText, fmt.Sprintf("%s/$1", s.autocompleteProjectMappings[p.AppName]))
+		p.UserText = replaceAmbiguousIssueReferences(s.autocompleteProjectMappings[p.AppName], p.UserText)
 	}
 
 	resp, err := s.saveReport(req.Context(), *p, reportDir, listingURL)
diff --git a/submit_test.go b/submit_test.go
index f5cca86..499d1b8 100644
--- a/submit_test.go
+++ b/submit_test.go
@@ -1,5 +1,6 @@
 /*
 Copyright 2017 Vector Creations Ltd
+Copyright 2020 The Matrix.org Foundation C.I.C.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -483,3 +484,20 @@ user_id: id
 		}
 	}
 }
+
+func TestAutocompleteIssueReferences(t *testing.T) {
+	tests := map[string]string{
+		"Testing #123 Foobar": "Testing owner/repo#123 Foobar", // standard
+		"#123":                "owner/repo#123",                // first/last word
+		"test (#123) bar":     "test (owner/repo#123) bar",     // brackets
+		"Start #123. Now":     "Start owner/repo#123. Now",     // followed by punctuation
+		"#123foo":             "#123foo",                       // ignore
+	}
+
+	for text, expect := range tests {
+		got := replaceAmbiguousIssueReferences("owner/repo", text)
+		if expect != got {
+			t.Errorf("expected %s got %s", expect, got)
+		}
+	}
+}