Sync with QuickBooks Online. Modernize Check Payments.

Fully integrated with QuickBooks Online, Checkrun enhances the accounts payable experience by delivering additional multi-layered security and fraud protection, digitally-driven convenience and mobile based approvals for the most modern way to cut checks.

Checkrun mobile app for business payments

Combine the power of QuickBooks Online & Checkrun

Checkrun works alongside QuickBooks Online, powering it up with real-time, two-way sync to record every payment and simplify your bill pay. Syncing Checkrun and QuickBooks Online saves time and eliminates double data entry. Checkrun pulls the payment and vendor information from QuickBooks, so you don’t have to manually enter bill details.

Once you’ve completed a payment in Checkrun, your QuickBooks Online account is updated with the payment details. That means you can track and monitor payments and approvals at any given moment. Learn more about how to connect Checkrun and QuickBooks Online in our help center.

Key benefits of integrating Checkrun with QuickBooks Online

A two-way sync between Checkrun and your QuickBooks Online account automatically adds all bills, invoices, supporting attachments, and payments into Checkrun – eliminating double data entry. Checkrun helps you streamline your back-office to eliminate manual work and reduce error. 

Manage multiple accounts in one place

A quick and simple set up and no duplicate data entry—ever. Checkrun supports quickly toggling between all of your clients Checkrun memberships with a single login.

Streamline accounts payable in one place

Manage check payments and printing in the cloud. Plus you can easily send a PDF of your printed checks to your QuickBooks Online account for record keeping.

Print checks when and how you want them

Whether it’s pre-prints or blank check stock, Checkrun accommodates multiple print layouts (top, middle, bottom), colors, and logos so you can customize payments to suit your needs.


Meet Your New Business Payment Wingman

Gone are the days of having to chase down check signatures, manage accounts across multiple programs, or spend hours preparing audit reports. Enhance the accounts payable process and streamline your workflow—from the Mobile App for signing checks and multi-layered security features to its seamless integration with QuickBooks Online to manage clients, payments and more. The Checkrun experience is friendly, cost-effective, and reliable—created for the way you want to work.

Powerful tools for QuickBooks Online

Great alone, better together. Experience powerful features with Checkrun and QuickBooks Online that will drive value and growth for your team and for your clients. Save time and increase organization, control and efficiency with Checkrun.

Vendor managment

The Checkrun dashboard gives you an overview of all of your clients and payment data. Easily switch between accounts and see a complete rundown into your  payments in one easy-to-use platform.

Custom approval workflows

Eliminate errors by creating and following approval payment workflows that match your business processes. Reminders can be sent at any time and our easy-to-use dashboard displays every bill in one place.

Audit trails

A built-in audit trail keeps track of every interaction a team member has with a bill or vendor – the best way to manage cash flow and keep payments secure.

Fraud detection

With features like Positive Pay, check fraud detection, and an audit trail on every bill, Checkrun is designed to keep you and your business safe.

Electronic remittance advice

Create visibility and build trust with your vendors with electronic remittance advice. All payment-related activity is automatically logged and attached to each payment for easy reference.


Checkrun automatically pulls all payment details, invoices, and attachments from QuickBooks Online for easy visibility and access in one place.


Checkrun + QuickBooks Online:
Modernize They Way You Pay By Check

Eliminate dual data entry with automatic two-way sync for all your bills and bill payments with QuickBooks Online.

Streamline your payment process

Checkrun syncs everything from QuickBooks Online; payment data like bills and invoices. You can even view attachments and track deadlines in real-time, from any device. Checkrun reconciles your bill payments back into your QuickBooks Online account with a full audit trail for each payment.

Send electronic remittance advice

On your end, the system automatically updates QuickBooks Online, so there is no need to manually track your payments. Your vendor will receive a remittance advice email confirming the details of the payment you sent.

Secure check printing and mailing 

Use Checkrun to approve, sign, and print checks from any device. You decide to print them yourself or let us handle it for you. Choose from multiple check layouts, add your business logo, electronically sign every check and more.

Use blank check stock and save!

Save 80% on the cost of preprinted QuickBooks checks when you switch to blank check stock. It’s easier, less expensive and more secure—plus, you can use one stock for all your payments.

Checkrun Mobile App

Businesses trust us to streamline their payables.

“Check signer can approve checks remotely, no need to come into the office just to sign checks. Able to use existing printed check stock. The customer service was awesome when setting up our account.”

Gayle K. 


“Very user friendly product & support staff is outstanding! Provides the trifecta: an approval workflow, the ability to print your own checks on blank paper or they will print & mail for you.”

Maleia F. 

CPA Firm Pro Advisor

“Love that we can write checks in QBO and send for approval electronically. Makes dual signatures so much easier to manage when you’re not in the same office.”

Jackie G. 


Frequently Asked Questions

What accounting systems does Checkrun sync with?

Checkrun is a cloud based application that works only with QuickBooks Online.

Does Checkrun provide help is setting up sync or integration with my accounting system?

At Checkrun, our dedicated team of experts is here to assist you and answer any questions or concerns you may have. We also offer chat support (with a short response time!) on our website and have a Help Center packed with helpful articles and tutorial videos.

Is it easy to use Checkrun to print checks in QuickBooks Online?

Yes, it’s extremely easy to print checks in QuickBooks Online with Checkrun. Find out more about our check writing and printing services here: business check printing for QuickBooks Online.

Is there a free trial of Checkrun?

Yes, Checkrun offers a 15-day risk-free trial with every membership. Credit card is required.

Get In Touch or Book a Demo

Ready to Get Started?

Join the hundreds of businesses choosing Checkrun to simplify accounts payable and business bill pay.

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