diff --git a/packages/cloudflare/src/client.ts b/packages/cloudflare/src/client.ts
index 3b4f591d5e22..bef4f0536d47 100644
--- a/packages/cloudflare/src/client.ts
+++ b/packages/cloudflare/src/client.ts
@@ -1,4 +1,4 @@
-import type { ClientOptions, Options, TracePropagationTargets } from '@sentry/core';
+import type { CheckIn, ClientOptions, MonitorConfig, Options, Scope, TracePropagationTargets } from '@sentry/core';
 import {
   _INTERNAL_clearAiProviderSkips,
   _INTERNAL_flushLogsBuffer,
@@ -163,6 +163,20 @@ export class CloudflareClient extends ServerRuntimeClient {
     }
   }
 
+  /**
+   * Sends the check-in at once instead of holding it for the flush at the end of the invocation.
+   * An `in_progress` check-in of a run that is longer than the check-in margin would otherwise
+   * reach Sentry too late, and Sentry would mark the run as missed.
+   */
+  public override captureCheckIn(checkIn: CheckIn, monitorConfig?: MonitorConfig, scope?: Scope): string {
+    const checkInId = super.captureCheckIn(checkIn, monitorConfig, scope);
+    const transport = this.getTransport();
+    if (transport) {
+      this._registerWithInvocationWaitUntil(transport.flush(2000));
+    }
+    return checkInId;
+  }
+
   /**
    * Disposes of the client and releases all resources.
    *
diff --git a/packages/cloudflare/src/instrumentations/worker/instrumentScheduled.ts b/packages/cloudflare/src/instrumentations/worker/instrumentScheduled.ts
index 8bf690d05175..8285830b73c1 100644
--- a/packages/cloudflare/src/instrumentations/worker/instrumentScheduled.ts
+++ b/packages/cloudflare/src/instrumentations/worker/instrumentScheduled.ts
@@ -65,11 +65,6 @@ function wrapScheduledHandler(
           finishCheckIn = client
             ?.getIntegrationByName<CronTriggersIntegration>('CronTriggers')
             ?.startCheckIn(controller.cron);
-          // The transport holds envelopes until the flush after the handler, so a run that is longer than
-          // the check-in margin would deliver its in_progress check-in too late and show as missed.
-          if (finishCheckIn) {
-            waitUntil(Promise.resolve(client?.getTransport()?.flush(2000)).catch(() => undefined));
-          }
         } catch (e) {
           DEBUG_BUILD && debug.warn('Failed to send the in_progress cron check-in', e);
         }
diff --git a/packages/cloudflare/src/integrations/cronTriggers.ts b/packages/cloudflare/src/integrations/cronTriggers.ts
index 289cfd18c849..4f49824018c1 100644
--- a/packages/cloudflare/src/integrations/cronTriggers.ts
+++ b/packages/cloudflare/src/integrations/cronTriggers.ts
@@ -139,8 +139,6 @@ const _cronTriggersIntegration = ((options: CronTriggersOptions = {}): CronTrigg
           );
       }
 
-      // Check-ins are captured directly rather than through `withMonitor`, which would fork the
-      // isolation scope and lose the invocation state attached to it.
       const checkInId = captureCheckIn(
         { monitorSlug, status: 'in_progress' },
         crontab ? { ...monitorSettings, schedule: { type: 'crontab', value: crontab } } : undefined,
diff --git a/packages/cloudflare/src/transport.ts b/packages/cloudflare/src/transport.ts
index b7f5a3181680..ee7bcce7730b 100644
--- a/packages/cloudflare/src/transport.ts
+++ b/packages/cloudflare/src/transport.ts
@@ -66,12 +66,16 @@ export class IsolatedPromiseBuffer {
 
     const drainController = new AbortController();
     this.drainSignal = drainController.signal;
-    let tasks: PromiseLike<TransportMakeRequestResponse>[];
-    try {
-      tasks = oldTaskProducers.map(taskProducer => taskProducer());
-    } finally {
-      this.drainSignal = undefined;
-    }
+    const tasks = oldTaskProducers.map(taskProducer => {
+      // A request that throws synchronously, such as a custom `fetch`, must not stop the other requests
+      // or throw into the caller.
+      try {
+        return taskProducer();
+      } catch (error) {
+        return Promise.reject(error);
+      }
+    });
+    this.drainSignal = undefined;
 
     return new Promise(resolve => {
       const timer = setTimeout(() => {
diff --git a/packages/cloudflare/src/utils/invocationContext.ts b/packages/cloudflare/src/utils/invocationContext.ts
index 5c343c3bd88a..aa2f55482a2f 100644
--- a/packages/cloudflare/src/utils/invocationContext.ts
+++ b/packages/cloudflare/src/utils/invocationContext.ts
@@ -16,8 +16,9 @@ import { getOriginalWaitUntil } from '../flush';
  *
  * The state rides on the invocation's forked isolation scope, which the async
  * context strategy (AsyncLocalStorage) hands back for exactly the async context that
- * owns the invocation — including detached continuations created inside it. A symbol
- * key keeps it off `Scope.clone()` and out of serialized event data.
+ * owns the invocation — including detached continuations created inside it. It lives under
+ * a symbol key in the scope's `refs`, so isolation scopes forked inside the invocation
+ * (`withMonitor`, `withIsolationScope`) share it, and it stays out of serialized event data.
  */
 export interface InvocationState {
   /**
@@ -63,7 +64,7 @@ export function getInvocationWaitUntil(state: InvocationState): ExecutionContext
   return state.waitUntil ?? undefined;
 }
 
-type ScopeWithInvocationState = Scope & {
+type ScopeRefsWithInvocationState = Scope['refs'] & {
   [INVOCATION_STATE]?: InvocationState;
 };
 
@@ -81,7 +82,7 @@ export function setInvocationState(scope: Scope, state: InvocationState): void {
     return;
   }
 
-  (scope as ScopeWithInvocationState)[INVOCATION_STATE] = state;
+  (scope.refs as ScopeRefsWithInvocationState)[INVOCATION_STATE] = state;
 }
 
 /**
@@ -91,9 +92,9 @@ export function setInvocationState(scope: Scope, state: InvocationState): void {
  * is never attached there in the first place).
  */
 export function getInvocationState(): InvocationState | undefined {
-  const isolationScope = getIsolationScope() as ScopeWithInvocationState;
+  const isolationScope = getIsolationScope();
   if (isolationScope === getDefaultIsolationScope()) {
     return undefined;
   }
-  return isolationScope[INVOCATION_STATE];
+  return (isolationScope.refs as ScopeRefsWithInvocationState)[INVOCATION_STATE];
 }
diff --git a/packages/cloudflare/test/client.test.ts b/packages/cloudflare/test/client.test.ts
index 2d7828be238d..27d0eae75835 100644
--- a/packages/cloudflare/test/client.test.ts
+++ b/packages/cloudflare/test/client.test.ts
@@ -2,6 +2,7 @@ import { beforeAll, beforeEach, describe, expect, it, vi } from 'vitest';
 import { setAsyncLocalStorageAsyncContextStrategy } from '@sentry/server-utils/no-diagnostic-channels';
 import { CloudflareClient, type CloudflareClientOptions } from '../src/client';
 import { makeFlushLock } from '../src/flush';
+import { makeCloudflareTransport } from '../src/transport';
 import { getInvocationState } from '../src/utils/invocationContext';
 import { withInvocationIsolationScope } from '../src/utils/invocationScope';
 
@@ -797,4 +798,50 @@ describe('CloudflareClient', () => {
       expect(flushSpy).not.toHaveBeenCalled();
     });
   });
+
+  describe('check-in delivery', () => {
+    it.each([true, false])(
+      'drains the transport for a check-in before the flush point and registers it with the invocation waitUntil (cacheClient: %s)',
+      cacheClient => {
+        const flushMock = vi.fn().mockResolvedValue(true);
+        const client = new CloudflareClient({
+          ...MOCK_CLIENT_OPTIONS,
+          cacheClient,
+          transport: () => ({ send: vi.fn().mockResolvedValue({}), flush: flushMock }),
+        });
+        client.init();
+        const ctx = { waitUntil: vi.fn(), passThroughOnException: vi.fn() };
+
+        withInvocationIsolationScope(() => {
+          client.captureCheckIn({ monitorSlug: 'foo', status: 'in_progress' });
+        }, ctx as never);
+
+        expect(flushMock).toHaveBeenCalledTimes(1);
+        expect(ctx.waitUntil).toHaveBeenCalledTimes(1);
+        expect(ctx.waitUntil).toHaveBeenCalledWith(expect.any(Promise));
+      },
+    );
+
+    it('does not throw when the fetch of the transport throws synchronously', async () => {
+      const client = new CloudflareClient({
+        ...MOCK_CLIENT_OPTIONS,
+        transport: makeCloudflareTransport,
+        transportOptions: {
+          fetch: () => {
+            throw new Error('foo');
+          },
+        },
+      });
+      client.init();
+      const waits: Promise<unknown>[] = [];
+      const ctx = { waitUntil: vi.fn(promise => waits.push(promise)), passThroughOnException: vi.fn() };
+
+      withInvocationIsolationScope(() => {
+        expect(() => client.captureCheckIn({ monitorSlug: 'foo', status: 'in_progress' })).not.toThrow();
+      }, ctx as never);
+
+      expect(waits).toHaveLength(1);
+      await expect(Promise.all(waits)).resolves.toBeDefined();
+    });
+  });
 });
diff --git a/packages/cloudflare/test/instrumentations/worker/instrumentScheduled.test.ts b/packages/cloudflare/test/instrumentations/worker/instrumentScheduled.test.ts
index 33649a188f06..843683be8925 100644
--- a/packages/cloudflare/test/instrumentations/worker/instrumentScheduled.test.ts
+++ b/packages/cloudflare/test/instrumentations/worker/instrumentScheduled.test.ts
@@ -2,7 +2,7 @@
 // Although this is not ideal, this is the best we can do until we have a better way to test cloudflare workers.
 
 import type { ExecutionContext, ScheduledController } from '@cloudflare/workers-types';
-import type { Event, Integration } from '@sentry/core';
+import type { Event, Integration, SerializedCheckIn } from '@sentry/core';
 import * as SentryCore from '@sentry/core';
 import { beforeEach, describe, expect, onTestFinished, test, vi } from 'vitest';
 import { CloudflareClient } from '../../../src/client';
@@ -478,6 +478,59 @@ describe('instrumentScheduled', () => {
       expect(sentItemTypes.filter(type => type === 'check_in')).toHaveLength(2);
     });
 
+    test('sends the in_progress check-in of withMonitor while its callback runs', async () => {
+      vi.useFakeTimers();
+      onTestFinished(() => {
+        vi.useRealTimers();
+      });
+      // Like the Cloudflare transport, this transport holds each envelope until it is drained.
+      const queued: string[] = [];
+      const delivered: string[] = [];
+      const waits: Promise<unknown>[] = [];
+      const wrappedHandler = withSentry(
+        env => ({
+          dsn: env.SENTRY_DSN,
+          transport: () => ({
+            send: async envelope => {
+              for (const [itemHeader, item] of envelope[1]) {
+                if (itemHeader.type === 'check_in') {
+                  queued.push((item as SerializedCheckIn).status);
+                }
+              }
+              return {};
+            },
+            flush: async () => {
+              delivered.push(...queued.splice(0));
+              return true;
+            },
+          }),
+        }),
+        {
+          async scheduled() {
+            await SentryCore.withMonitor('foo', () => new Promise(resolve => setTimeout(resolve, 5 * 60_000)), {
+              schedule: { type: 'crontab', value: '30 9 * * *' },
+              checkinMargin: 1,
+            });
+          },
+        } satisfies ExportedHandler<typeof MOCK_ENV>,
+      );
+
+      const run = wrappedHandler.scheduled?.(controllerFor('30 9 * * 1-5'), MOCK_ENV, {
+        waitUntil: vi.fn(promise => waits.push(promise)),
+        passThroughOnException: vi.fn(),
+      } as unknown as ExecutionContext);
+
+      await vi.advanceTimersByTimeAsync(60_000);
+      expect(delivered).toEqual(['in_progress']);
+      expect(waits).toHaveLength(1);
+
+      await vi.advanceTimersByTimeAsync(4 * 60_000);
+      await run;
+      await vi.runAllTimersAsync();
+      await Promise.all(waits);
+      expect(delivered).toEqual(['in_progress', 'ok']);
+    });
+
     test('drains the transport for the in_progress check-in while the handler runs', async () => {
       const transportFlush = vi.fn(async () => true);
       let finishHandler: () => void = () => undefined;
diff --git a/packages/cloudflare/test/transport.test.ts b/packages/cloudflare/test/transport.test.ts
index 1750176f5591..3fa9f99f157f 100644
--- a/packages/cloudflare/test/transport.test.ts
+++ b/packages/cloudflare/test/transport.test.ts
@@ -1,4 +1,4 @@
-import type { EventEnvelope, EventItem } from '@sentry/core';
+import type { EventEnvelope, EventItem, TransportMakeRequestResponse } from '@sentry/core';
 import { createEnvelope, SENTRY_BUFFER_FULL_ERROR, serializeEnvelope } from '@sentry/core';
 import { afterAll, describe, expect, it, vi } from 'vitest';
 import type { CloudflareTransportOptions } from '../src/transport';
@@ -236,6 +236,22 @@ describe('IsolatedPromiseBuffer', () => {
     expect(task2).toHaveBeenCalled();
   });
 
+  it('runs the other tasks of a drain when one task throws synchronously', async () => {
+    const ipb = new IsolatedPromiseBuffer();
+
+    const task1 = vi.fn((): Promise<TransportMakeRequestResponse> => {
+      throw new Error('foo');
+    });
+    const task2 = vi.fn(() => Promise.resolve({}));
+
+    await ipb.add(task1);
+    await ipb.add(task2);
+
+    await expect(ipb.drain()).resolves.toEqual(true);
+
+    expect(task2).toHaveBeenCalled();
+  });
+
   it('should allow for a custom fetch function to be passed in', async () => {
     const customFetch = vi.fn(async () => {
       return {
diff --git a/packages/cloudflare/test/utils/invocationContext.test.ts b/packages/cloudflare/test/utils/invocationContext.test.ts
index cd05ebf6b8cd..3378f75dfdfb 100644
--- a/packages/cloudflare/test/utils/invocationContext.test.ts
+++ b/packages/cloudflare/test/utils/invocationContext.test.ts
@@ -48,13 +48,16 @@ describe('invocation state', () => {
     expect(getInvocationState()).toBeUndefined();
   });
 
-  it('is not inherited by scope clones', () => {
-    const scope = getDefaultIsolationScope().clone();
-    setInvocationState(scope, { ctx: undefined });
+  it('is shared with isolation scopes forked inside the invocation', () => {
+    const ctx = { waitUntil: vi.fn(), passThroughOnException: vi.fn() };
 
-    withIsolationScope(scope.clone(), () => {
-      expect(getInvocationState()).toBeUndefined();
-    });
+    withInvocationIsolationScope(() => {
+      const state = getInvocationState();
+
+      withIsolationScope(() => {
+        expect(getInvocationState()).toBe(state);
+      });
+    }, ctx);
   });
 
   it('is attached at the invocation entry point and kept when reentrant', () => {