diff --git a/lfsapi/endpoint_finder.go b/lfsapi/endpoint_finder.go
index efdd1e80..5861d79f 100644
--- a/lfsapi/endpoint_finder.go
+++ b/lfsapi/endpoint_finder.go
@@ -335,10 +335,11 @@ func initAliases(e *endpointGitFinder, git config.Environment) {
 
 func storeAlias(aliases map[string]string, key string, values []string, suffix string) {
 	for _, value := range values {
-		if _, ok := aliases[value]; ok {
+		url := key[len(aliasPrefix) : len(key)-len(suffix)]
+		if v, ok := aliases[value]; ok && v != url {
 			fmt.Fprintf(os.Stderr, "WARNING: Multiple 'url.*.%s' keys with the same alias: %q\n", suffix, value)
 		}
-		aliases[value] = key[len(aliasPrefix) : len(key)-len(suffix)]
+		aliases[value] = url
 	}
 }
 
diff --git a/t/t-env.sh b/t/t-env.sh
index 6347002b..b41e4a30 100755
--- a/t/t-env.sh
+++ b/t/t-env.sh
@@ -1040,3 +1040,41 @@ UploadTransfers=basic,lfs-standalone-file
   contains_same_elements "$expected" "$actual"
 )
 end_test
+
+begin_test "env with duplicate endpoints"
+(
+  set -e
+  reponame="env-duplicate-endpoints"
+  unset_vars
+  mkdir $reponame
+  cd $reponame
+  git init
+  git remote add origin "$GITSERVER/env-origin-remote"
+  git remote add other "$GITSERVER/env-other-remote"
+
+  touch a.txt
+  git add a.txt
+  git commit -m "initial commit"
+
+  cat <<EOF >>.git/config
+[url "https://host.example/domain/"]
+	insteadOf = git@host.example:domain/
+[url "https://host.example/domain/"]
+	insteadOf = git@host.example:domain/
+EOF
+
+  git lfs env 2>&1 | tee test.log
+  if grep 'WARNING.*same alias' test.log
+  then
+    exit 1
+  fi
+
+  cat <<EOF >>.git/config
+[url "https://somewhere-else.example/domain/"]
+	insteadOf = git@host.example:domain/
+EOF
+
+  git lfs env 2>&1 | tee test.log
+  grep 'WARNING.*same alias' test.log
+)
+end_test