diff --git a/src/modes/agent/parse-tools.ts b/src/modes/agent/parse-tools.ts
index 9b2fdcb90..639c9131a 100644
--- a/src/modes/agent/parse-tools.ts
+++ b/src/modes/agent/parse-tools.ts
@@ -1,22 +1,33 @@
 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+"([^"]+)"/, // Double quoted
-    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/, // Single quoted
-    /--(?:allowedTools|allowed-tools)\s+([^\s]+)/, // Unquoted
+    /--(?: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)
   ];
 
+  const tools: string[] = [];
+  const seen = new Set<string>();
+
   for (const pattern of patterns) {
-    const match = claudeArgs.match(pattern);
-    if (match && match[1]) {
-      // Don't return if the value starts with -- (another flag)
-      if (match[1].startsWith("--")) {
-        return [];
+    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);
+          }
+        }
       }
-      return match[1].split(",").map((t) => t.trim());
     }
   }
 
-  return [];
+  return tools;
 }
diff --git a/test/modes/parse-tools.test.ts b/test/modes/parse-tools.test.ts
index e88e8001c..84916fb13 100644
--- a/test/modes/parse-tools.test.ts
+++ b/test/modes/parse-tools.test.ts
@@ -35,12 +35,44 @@ describe("parseAllowedTools", () => {
     expect(parseAllowedTools("")).toEqual([]);
   });
 
-  test("handles duplicate --allowedTools flags", () => {
+  test("handles --allowedTools followed by another --allowedTools flag", () => {
     const args = "--allowedTools --allowedTools mcp__github__*";
-    // Should not match the first one since the value is another flag
+    // 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([]);
   });
 
+  test("parses multiple separate --allowed-tools flags", () => {
+    const args =
+      "--allowed-tools 'mcp__context7__*' --allowed-tools 'Read,Glob' --allowed-tools 'mcp__github_inline_comment__*'";
+    expect(parseAllowedTools(args)).toEqual([
+      "mcp__context7__*",
+      "Read",
+      "Glob",
+      "mcp__github_inline_comment__*",
+    ]);
+  });
+
+  test("parses multiple --allowed-tools flags on separate lines", () => {
+    const args = `--model 'claude-haiku'
+--allowed-tools 'mcp__context7__*'
+--allowed-tools 'Read,Glob,Grep'
+--allowed-tools 'mcp__github_inline_comment__create_inline_comment'`;
+    expect(parseAllowedTools(args)).toEqual([
+      "mcp__context7__*",
+      "Read",
+      "Glob",
+      "Grep",
+      "mcp__github_inline_comment__create_inline_comment",
+    ]);
+  });
+
+  test("deduplicates tools from multiple flags", () => {
+    const args =
+      "--allowed-tools 'Read,Glob' --allowed-tools 'Glob,Grep' --allowed-tools 'Read'";
+    expect(parseAllowedTools(args)).toEqual(["Read", "Glob", "Grep"]);
+  });
+
   test("handles typo --alloedTools", () => {
     const args = "--alloedTools mcp__github__*";
     expect(parseAllowedTools(args)).toEqual([]);