diff --git a/src/integrations/claude-code/__tests__/run.spec.ts b/src/integrations/claude-code/__tests__/run.spec.ts
index a07120c28a..7f738c834a 100644
--- a/src/integrations/claude-code/__tests__/run.spec.ts
+++ b/src/integrations/claude-code/__tests__/run.spec.ts
@@ -139,7 +139,7 @@ describe("runClaudeCode", () => {
 		expect(typeof result[Symbol.asyncIterator]).toBe("function")
 	})
 
-	test("should handle platform-specific stdin behavior", async () => {
+	test("should always pass system prompt via flag and messages via stdin", async () => {
 		const { runClaudeCode } = await import("../run")
 		const messages = [{ role: "user" as const, content: "Hello world!" }]
 		const systemPrompt = "You are a helpful assistant"
@@ -158,12 +158,13 @@ describe("runClaudeCode", () => {
 			results.push(chunk)
 		}
 
-		// On Windows, should NOT have --system-prompt in args
+		// On Windows, should now ALWAYS have --system-prompt in args
 		const [, args] = mockExeca.mock.calls[0]
-		expect(args).not.toContain("--system-prompt")
+		expect(args).toContain("--system-prompt")
+		expect(args).toContain(systemPrompt)
 
-		// Should pass both system prompt and messages via stdin
-		const expectedStdinData = JSON.stringify({ systemPrompt, messages })
+		// Should only pass messages via stdin (no longer includes system prompt)
+		const expectedStdinData = JSON.stringify(messages)
 		expect(mockStdin.write).toHaveBeenCalledWith(expectedStdinData, "utf8", expect.any(Function))
 
 		// Reset mocks for non-Windows test
@@ -179,12 +180,12 @@ describe("runClaudeCode", () => {
 			results2.push(chunk)
 		}
 
-		// On non-Windows, should have --system-prompt in args
+		// On non-Windows, should also have --system-prompt in args
 		const [, args2] = mockExeca.mock.calls[0]
 		expect(args2).toContain("--system-prompt")
 		expect(args2).toContain(systemPrompt)
 
-		// Should only pass messages via stdin
+		// Should only pass messages via stdin (consistent across platforms)
 		expect(mockStdin.write).toHaveBeenCalledWith(JSON.stringify(messages), "utf8", expect.any(Function))
 	})
 
diff --git a/src/integrations/claude-code/run.ts b/src/integrations/claude-code/run.ts
index 1d617b9242..521ad02d16 100644
--- a/src/integrations/claude-code/run.ts
+++ b/src/integrations/claude-code/run.ts
@@ -154,15 +154,9 @@ function runProcess({
 	maxOutputTokens,
 }: ClaudeCodeOptions & { maxOutputTokens?: number }) {
 	const claudePath = path || "claude"
-	const isWindows = os.platform() === "win32"
 
-	// Build args based on platform
-	const args = ["-p"]
-
-	// Pass system prompt as flag on non-Windows, via stdin on Windows (avoids cmd length limits)
-	if (!isWindows) {
-		args.push("--system-prompt", systemPrompt)
-	}
+	// Build args - always pass system prompt as flag to avoid mixing with Claude Code's default
+	const args = ["-p", "--system-prompt", systemPrompt]
 
 	args.push(
 		"--verbose",
@@ -196,17 +190,9 @@ function runProcess({
 		timeout: CLAUDE_CODE_TIMEOUT,
 	})
 
-	// Prepare stdin data: Windows gets both system prompt & messages (avoids 8191 char limit),
-	// other platforms get messages only (avoids Linux E2BIG error from ~128KiB execve limit)
-	let stdinData: string
-	if (isWindows) {
-		stdinData = JSON.stringify({
-			systemPrompt,
-			messages,
-		})
-	} else {
-		stdinData = JSON.stringify(messages)
-	}
+	// Prepare stdin data: only send messages to avoid E2BIG errors
+	// System prompt is now always passed via --system-prompt flag
+	const stdinData = JSON.stringify(messages)
 
 	// Use setImmediate to ensure process is spawned before writing (prevents stdin race conditions)
 	setImmediate(() => {