diff --git a/src/create-prompt/index.ts b/src/create-prompt/index.ts
index f622dec..9a91110 100644
--- a/src/create-prompt/index.ts
+++ b/src/create-prompt/index.ts
@@ -58,10 +58,27 @@ export function buildAllowedToolsString(
 
 export function buildDisallowedToolsString(
   customDisallowedTools?: string,
+  allowedTools?: string,
 ): string {
-  let allDisallowedTools = DISALLOWED_TOOLS.join(",");
+  let disallowedTools = [...DISALLOWED_TOOLS];
+
+  // If user has explicitly allowed some hardcoded disallowed tools, remove them from disallowed list
+  if (allowedTools) {
+    const allowedToolsArray = allowedTools
+      .split(",")
+      .map((tool) => tool.trim());
+    disallowedTools = disallowedTools.filter(
+      (tool) => !allowedToolsArray.includes(tool),
+    );
+  }
+
+  let allDisallowedTools = disallowedTools.join(",");
   if (customDisallowedTools) {
-    allDisallowedTools = `${allDisallowedTools},${customDisallowedTools}`;
+    if (allDisallowedTools) {
+      allDisallowedTools = `${allDisallowedTools},${customDisallowedTools}`;
+    } else {
+      allDisallowedTools = customDisallowedTools;
+    }
   }
   return allDisallowedTools;
 }
@@ -648,6 +665,7 @@ export async function createPrompt(
     );
     const allDisallowedTools = buildDisallowedToolsString(
       preparedContext.disallowedTools,
+      preparedContext.allowedTools,
     );
 
     core.exportVariable("ALLOWED_TOOLS", allAllowedTools);
diff --git a/test/create-prompt.test.ts b/test/create-prompt.test.ts
index 3985011..3eb493d 100644
--- a/test/create-prompt.test.ts
+++ b/test/create-prompt.test.ts
@@ -722,4 +722,51 @@ describe("buildDisallowedToolsString", () => {
     expect(parts).toContain("BadTool1");
     expect(parts).toContain("BadTool2");
   });
+
+  test("should remove hardcoded disallowed tools if they are in allowed tools", () => {
+    const customDisallowedTools = "BadTool1,BadTool2";
+    const allowedTools = "WebSearch,SomeOtherTool";
+    const result = buildDisallowedToolsString(
+      customDisallowedTools,
+      allowedTools,
+    );
+
+    // WebSearch should be removed from disallowed since it's in allowed
+    expect(result).not.toContain("WebSearch");
+
+    // WebFetch should still be disallowed since it's not in allowed
+    expect(result).toContain("WebFetch");
+
+    // Custom disallowed tools should still be present
+    expect(result).toContain("BadTool1");
+    expect(result).toContain("BadTool2");
+  });
+
+  test("should remove all hardcoded disallowed tools if they are all in allowed tools", () => {
+    const allowedTools = "WebSearch,WebFetch,SomeOtherTool";
+    const result = buildDisallowedToolsString(undefined, allowedTools);
+
+    // Both hardcoded disallowed tools should be removed
+    expect(result).not.toContain("WebSearch");
+    expect(result).not.toContain("WebFetch");
+
+    // Result should be empty since no custom disallowed tools provided
+    expect(result).toBe("");
+  });
+
+  test("should handle custom disallowed tools when all hardcoded tools are overridden", () => {
+    const customDisallowedTools = "BadTool1,BadTool2";
+    const allowedTools = "WebSearch,WebFetch";
+    const result = buildDisallowedToolsString(
+      customDisallowedTools,
+      allowedTools,
+    );
+
+    // Hardcoded tools should be removed
+    expect(result).not.toContain("WebSearch");
+    expect(result).not.toContain("WebFetch");
+
+    // Only custom disallowed tools should remain
+    expect(result).toBe("BadTool1,BadTool2");
+  });
 });