diff --git a/src/automation/autonomousRunner.cancel.test.ts b/src/automation/autonomousRunner.cancel.test.ts
index 3ac473b..0e7e14b 100644
--- a/src/automation/autonomousRunner.cancel.test.ts
+++ b/src/automation/autonomousRunner.cancel.test.ts
@@ -62,7 +62,11 @@ describe('AutonomousRunner cancellation state sync', () => {
   beforeEach(async () => {
     vi.resetModules();
     tempDir = mkdtempSync(join(tmpdir(), 'openswarm-cancel-sync-'));
-    vi.stubEnv('OPENSWARM_TASK_STATE_FILE', join(tempDir, 'task-state.json'));
+    vi.stubEnv('OPENSWARM_TASK_STATE_FILE', join(tempDir, 'task-state.json')); // canonical store (taskState/store)
+    vi.stubEnv('OPENSWARM_RUNNER_TASK_STATE_FILE', join(tempDir, 'runner-task-state.json')); // legacy runnerState
+    vi.stubEnv('OPENSWARM_RUNNER_REJECTION_STATE_FILE', join(tempDir, 'runner-rejection-state.json'));
+    vi.stubEnv('OPENSWARM_RUNNER_PIPELINE_HISTORY_FILE', join(tempDir, 'runner-pipeline-history.json'));
+    vi.stubEnv('OPENSWARM_RUNNER_DECOMPOSITION_STATE_FILE', join(tempDir, 'runner-decomposition-state.json'));
     ({ AutonomousRunner } = await import('./autonomousRunner.js'));
     runnerExecution = await import('./runnerExecution.js');
     taskStateStore = await import('../taskState/store.js');
diff --git a/src/automation/autonomousRunner.infraError.test.ts b/src/automation/autonomousRunner.infraError.test.ts
index bce8d84..1921a92 100644
--- a/src/automation/autonomousRunner.infraError.test.ts
+++ b/src/automation/autonomousRunner.infraError.test.ts
@@ -74,7 +74,11 @@ describe('AutonomousRunner infra_error handling (INT-2010)', () => {
   beforeEach(async () => {
     vi.resetModules();
     tempDir = mkdtempSync(join(tmpdir(), 'openswarm-infra-'));
-    vi.stubEnv('OPENSWARM_TASK_STATE_FILE', join(tempDir, 'task-state.json'));
+    vi.stubEnv('OPENSWARM_TASK_STATE_FILE', join(tempDir, 'task-state.json')); // canonical store (taskState/store)
+    vi.stubEnv('OPENSWARM_RUNNER_TASK_STATE_FILE', join(tempDir, 'runner-task-state.json')); // legacy runnerState
+    vi.stubEnv('OPENSWARM_RUNNER_REJECTION_STATE_FILE', join(tempDir, 'runner-rejection-state.json'));
+    vi.stubEnv('OPENSWARM_RUNNER_PIPELINE_HISTORY_FILE', join(tempDir, 'runner-pipeline-history.json'));
+    vi.stubEnv('OPENSWARM_RUNNER_DECOMPOSITION_STATE_FILE', join(tempDir, 'runner-decomposition-state.json'));
     ({ AutonomousRunner } = await import('./autonomousRunner.js'));
     runnerExecution = await import('./runnerExecution.js');
   }, 30000);
diff --git a/src/automation/runnerState.coverage.test.ts b/src/automation/runnerState.coverage.test.ts
index 6dbe206..2e6f817 100644
--- a/src/automation/runnerState.coverage.test.ts
+++ b/src/automation/runnerState.coverage.test.ts
@@ -13,6 +13,12 @@ async function loadFreshModule() {
   tempHome = mkdtempSync(join(tmpdir(), 'openswarm-runner-state-'));
   vi.stubEnv('HOME', tempHome);
   vi.stubEnv('USERPROFILE', tempHome);
+  // Clear any RUNNER_* overrides inherited from the shell (e.g. CI) so every path
+  // derives from tempHome, independent of the ambient environment. (INT-2543)
+  for (const v of ['OPENSWARM_RUNNER_TASK_STATE_FILE', 'OPENSWARM_RUNNER_REJECTION_STATE_FILE',
+    'OPENSWARM_RUNNER_PIPELINE_HISTORY_FILE', 'OPENSWARM_RUNNER_DECOMPOSITION_STATE_FILE']) {
+    vi.stubEnv(v, '');
+  }
   mod = await import('./runnerState.js');
 }
 
@@ -206,3 +212,57 @@ it('pickFailureDetail skips locale noSummary fallbacks (INT-2504 follow-up)', ()
   expect(mod.pickFailureDetail(['(no summary)', 'real feedback here'])).toBe('real feedback here');
   expect(mod.pickFailureDetail(['(요약 없음)'])).toBeUndefined();
 });
+
+describe('state-file env overrides (INT-2543)', () => {
+  afterEach(() => vi.unstubAllEnvs());
+
+  it('honors the OPENSWARM_RUNNER_* overrides for all four state files (test isolation)', async () => {
+    vi.resetModules();
+    const taskPath = join(tmpdir(), 'ovr-int2543-task.json');
+    const rejPath = join(tmpdir(), 'ovr-int2543-rej.json');
+    const histPath = join(tmpdir(), 'ovr-int2543-hist.json');
+    const decompPath = join(tmpdir(), 'ovr-int2543-decomp.json');
+    vi.stubEnv('OPENSWARM_RUNNER_TASK_STATE_FILE', taskPath);
+    vi.stubEnv('OPENSWARM_RUNNER_REJECTION_STATE_FILE', rejPath);
+    vi.stubEnv('OPENSWARM_RUNNER_PIPELINE_HISTORY_FILE', histPath);
+    vi.stubEnv('OPENSWARM_RUNNER_DECOMPOSITION_STATE_FILE', decompPath);
+    const m = await import('./runnerState.js');
+    expect(m.TASK_STATE_FILE).toBe(taskPath);
+    expect(m.REJECTION_STATE_FILE).toBe(rejPath);
+    expect(m.PIPELINE_HISTORY_FILE).toBe(histPath);
+    expect(m.DECOMPOSITION_STATE_FILE).toBe(decompPath);
+  });
+
+  it('appendPipelineHistory writes ONLY to the overridden pipeline-history file', async () => {
+    vi.resetModules();
+    const histPath = join(tmpdir(), `ovr-int2543-hist-${process.pid}-write.json`);
+    if (existsSync(histPath)) rmSync(histPath);
+    vi.stubEnv('OPENSWARM_RUNNER_PIPELINE_HISTORY_FILE', histPath);
+    vi.stubEnv('HOME', mkdtempSync(join(tmpdir(), 'oh-'))); // guard: any leak lands here, not real ~/.claude
+    const m = await import('./runnerState.js');
+    m.appendPipelineHistory({ taskId: 't1', issueId: 'INT-X', title: 'x', finalStatus: 'approved', success: true, durationMs: 1, at: '2026-01-01T00:00:00Z' } as any);
+    expect(existsSync(histPath)).toBe(true); // the override path got the write
+    expect(JSON.parse(readFileSync(histPath, 'utf8')).length).toBe(1);
+  });
+
+  it('does NOT reuse the canonical store env var (would clobber taskState/store schema)', async () => {
+    vi.resetModules();
+    // Setting ONLY the canonical store's var must not move the legacy runner path —
+    // sharing it would let one store overwrite the other's differently-schema'd file.
+    vi.stubEnv('OPENSWARM_TASK_STATE_FILE', join(tmpdir(), 'canonical-store.json'));
+    vi.stubEnv('OPENSWARM_RUNNER_TASK_STATE_FILE', ''); // independent of ambient shell env
+    vi.stubEnv('HOME', '/tmp/fake-home-int2543');
+    vi.stubEnv('USERPROFILE', '/tmp/fake-home-int2543');
+    const m = await import('./runnerState.js');
+    expect(m.TASK_STATE_FILE).toBe('/tmp/fake-home-int2543/.claude/openswarm-task-state.json');
+  });
+
+  it('falls back to the ~/.claude default when the override is unset (backward compatible)', async () => {
+    vi.resetModules();
+    vi.stubEnv('OPENSWARM_RUNNER_TASK_STATE_FILE', ''); // empty → falsy → fallback
+    vi.stubEnv('HOME', '/tmp/fake-home-int2543');
+    vi.stubEnv('USERPROFILE', '/tmp/fake-home-int2543');
+    const m = await import('./runnerState.js');
+    expect(m.TASK_STATE_FILE).toBe('/tmp/fake-home-int2543/.claude/openswarm-task-state.json');
+  });
+});
diff --git a/src/automation/runnerState.ts b/src/automation/runnerState.ts
index b174908..3c73d49 100644
--- a/src/automation/runnerState.ts
+++ b/src/automation/runnerState.ts
@@ -17,10 +17,19 @@ export function isPathEnabled(resolvedPath: string, enabledProjects: Set<string>
   return false;
 }
 
-export const TASK_STATE_FILE = join(homedir(), '.claude', 'openswarm-task-state.json');
-export const PIPELINE_HISTORY_FILE = join(homedir(), '.claude', 'openswarm-pipeline-history.json');
-export const REJECTION_STATE_FILE = join(homedir(), '.claude', 'openswarm-rejection-state.json');
-export const DECOMPOSITION_STATE_FILE = join(homedir(), '.claude', 'openswarm-decomposition-state.json');
+// State-file paths honor env overrides so tests (and alternate deployments) can
+// redirect them off the real ~/.claude state — an unset override keeps the exact
+// legacy path (backward compatible). Without this, every runner integration test
+// wrote the LIVE daemon's state files (observed: ISSUE-1 accrued 184 phantom failures),
+// which also made those tests flaky. Read at import; tests stub the env then re-import.
+// NOTE: these use OPENSWARM_RUNNER_* names, deliberately DISTINCT from the canonical
+// task store's OPENSWARM_TASK_STATE_FILE (src/taskState/store.ts) — this legacy runner
+// state has a different schema ({completed,failed,retryTimes,…}), so sharing the env
+// var would let one store silently overwrite the other's file. (INT-2543)
+export const TASK_STATE_FILE = process.env.OPENSWARM_RUNNER_TASK_STATE_FILE || join(homedir(), '.claude', 'openswarm-task-state.json');
+export const PIPELINE_HISTORY_FILE = process.env.OPENSWARM_RUNNER_PIPELINE_HISTORY_FILE || join(homedir(), '.claude', 'openswarm-pipeline-history.json');
+export const REJECTION_STATE_FILE = process.env.OPENSWARM_RUNNER_REJECTION_STATE_FILE || join(homedir(), '.claude', 'openswarm-rejection-state.json');
+export const DECOMPOSITION_STATE_FILE = process.env.OPENSWARM_RUNNER_DECOMPOSITION_STATE_FILE || join(homedir(), '.claude', 'openswarm-decomposition-state.json');
 export const DAILY_PACE_FILE = join(homedir(), '.openswarm', 'daily-pace.json');
 export const PROJECT_SELECTION_FILE = join(homedir(), '.openswarm', 'project-selection.json');
 const MAX_PIPELINE_HISTORY = 100;