diff --git a/src/modes/agent/parse-tools.ts b/src/modes/agent/parse-tools.ts
index 639c9131..013fda5d 100644
--- a/src/modes/agent/parse-tools.ts
+++ b/src/modes/agent/parse-tools.ts
@@ -1,29 +1,77 @@
-export function parseAllowedTools(claudeArgs: string): string[] {
-  // Match --allowedTools or --allowed-tools followed by the value
-  // Handle both quoted and unquoted values
-  // Use /g flag to find ALL occurrences, not just the first one
-  const patterns = [
-    /--(?:allowedTools|allowed-tools)\s+"([^"]+)"/g, // Double quoted
-    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/g, // Single quoted
-    /--(?:allowedTools|allowed-tools)\s+([^'"\s][^\s]*)/g, // Unquoted (must not start with quote)
-  ];
+import { parse as parseShellArgs } from "shell-quote";
 
+// Flags whose values make up the allowed-tools list.
+// Include both camelCase and hyphenated variants for CLI compatibility.
+const ALLOWED_TOOLS_FLAGS = new Set(["allowedTools", "allowed-tools"]);
+
+/**
+ * Strip comment lines from a shell argument string.
+ * Lines whose first non-whitespace character is `#` are removed entirely.
+ * Mirrors stripShellComments in base-action/src/parse-sdk-options.ts.
+ */
+function stripShellComments(input: string): string {
+  return input
+    .split("\n")
+    .filter((line) => !line.trim().startsWith("#"))
+    .join("\n");
+}
+
+/**
+ * Tokenize a claude_args string the same way base-action/src/parse-sdk-options.ts
+ * does: strip full comment lines, then run shell-quote. shell-quote returns
+ * unquoted glob patterns (e.g. `mcp__github__*`) as `{ op: "glob", pattern }`
+ * objects rather than strings, so recover their literal text; drop operator
+ * tokens (`|`, `>`, `;`, ...) which carry no value.
+ */
+function tokenize(claudeArgs: string): string[] {
+  return parseShellArgs(stripShellComments(claudeArgs))
+    .map((token) => {
+      if (typeof token === "string") return token;
+      if (token && typeof token === "object" && "pattern" in token) {
+        return (token as { pattern: string }).pattern;
+      }
+      return null;
+    })
+    .filter((token): token is string => token !== null);
+}
+
+/**
+ * Parse the list of allowed tool names from a user-provided claude_args string.
+ *
+ * This is used to decide which GitHub MCP servers to install. It MUST stay in
+ * agreement with how the actual tool list is built for the SDK in
+ * base-action/src/parse-sdk-options.ts (parseClaudeArgsToExtraArgs): otherwise a
+ * tool can be granted to Claude without its MCP server being installed, or a
+ * server can be installed for a tool that was never granted (#1357).
+ *
+ * To stay in agreement it uses the same shell-quote tokenizer and the same
+ * "an accumulating flag consumes all consecutive non-flag values" semantics,
+ * so `--allowedTools "Read" "Grep" "mcp__github__get_commit"` captures all
+ * three values, and commented-out lines are ignored.
+ */
+export function parseAllowedTools(claudeArgs: string): string[] {
+  if (!claudeArgs?.trim()) return [];
+
+  const args = tokenize(claudeArgs);
   const tools: string[] = [];
   const seen = new Set<string>();
 
-  for (const pattern of patterns) {
-    for (const match of claudeArgs.matchAll(pattern)) {
-      if (match[1]) {
-        // Don't add if the value starts with -- (another flag)
-        if (match[1].startsWith("--")) {
-          continue;
-        }
-        for (const tool of match[1].split(",")) {
-          const trimmed = tool.trim();
-          if (trimmed && !seen.has(trimmed)) {
-            seen.add(trimmed);
-            tools.push(trimmed);
-          }
+  for (let i = 0; i < args.length; i++) {
+    const arg = args[i];
+    if (!arg?.startsWith("--")) continue;
+
+    const flag = arg.slice(2);
+    if (!ALLOWED_TOOLS_FLAGS.has(flag)) continue;
+
+    // Consume all consecutive non-flag values, e.g.
+    //   --allowedTools "Read" "Grep" "mcp__github__get_commit"
+    while (i + 1 < args.length && !args[i + 1]!.startsWith("--")) {
+      i++;
+      for (const tool of args[i]!.split(",")) {
+        const trimmed = tool.trim();
+        if (trimmed && !seen.has(trimmed)) {
+          seen.add(trimmed);
+          tools.push(trimmed);
         }
       }
     }
diff --git a/test/modes/parse-tools.test.ts b/test/modes/parse-tools.test.ts
index 84916fb1..cc854729 100644
--- a/test/modes/parse-tools.test.ts
+++ b/test/modes/parse-tools.test.ts
@@ -37,9 +37,43 @@ describe("parseAllowedTools", () => {
 
   test("handles --allowedTools followed by another --allowedTools flag", () => {
     const args = "--allowedTools --allowedTools mcp__github__*";
-    // The second --allowedTools is consumed as a value of the first, then skipped.
-    // This is an edge case with malformed input - returns empty.
-    expect(parseAllowedTools(args)).toEqual([]);
+    // The first --allowedTools has no value (the next token is another flag);
+    // the second consumes mcp__github__*. This matches how the SDK option
+    // parser (parse-sdk-options.ts) reads the same input.
+    expect(parseAllowedTools(args)).toEqual(["mcp__github__*"]);
+  });
+
+  test("captures multiple values after a single --allowedTools flag", () => {
+    // Regression for #1357: the install-decision parser must capture every
+    // value, not just the first, so it agrees with the tools actually granted
+    // to Claude. Previously only "Read" was seen, so the github MCP server was
+    // not installed even though mcp__github__get_commit was granted.
+    const args = '--allowedTools "Read" "Grep" "mcp__github__get_commit"';
+    expect(parseAllowedTools(args)).toEqual([
+      "Read",
+      "Grep",
+      "mcp__github__get_commit",
+    ]);
+  });
+
+  test("captures multiple values spread across lines under one flag", () => {
+    const args = `--allowedTools
+ "Read"
+ "Grep"
+ "mcp__github__get_commit"`;
+    expect(parseAllowedTools(args)).toEqual([
+      "Read",
+      "Grep",
+      "mcp__github__get_commit",
+    ]);
+  });
+
+  test("ignores commented-out lines", () => {
+    // Regression for #1357: a commented-out flag must not be counted, matching
+    // the SDK parser which strips comment lines before parsing.
+    const args = `# --allowedTools "mcp__github__get_commit"
+--allowedTools "Read"`;
+    expect(parseAllowedTools(args)).toEqual(["Read"]);
   });
 
   test("parses multiple separate --allowed-tools flags", () => {