The Accounts Payable Workflow in QuickBooks: How to Improve the Process

Are you relying on the current accounts payable (AP) workflow in QuickBooks Desktop or Online to manage your financial operations? If so, you’re not alone.

The QuickBooks AP workflow includes tasks like invoice receipt, data entry, approval, and payment required to manage AP within the software. However, while these AP workflow tasks in QuickBooks provide basic functionality, it falls short when it comes to advanced features tailored to modern AP. As a result, AP teams often complete manual, time-consuming tasks outside of QuickBooks, hindering both accuracy and efficiency.

With the right AP automation solution, organizations can reduce human error, capture invoice data more accurately, streamline approvals, optimize payment methods, and increase visibility through analytics and reporting. It’s time to take your QuickBooks AP workflow to the next level.

State of AP Report 2022 Download

An Overview of the AP Workflow in QuickBooks

The current AP workflow in QuickBooks, whether Online or Desktop, provides basic functionality for managing AP, such as entering and paying bills. But without more sophisticated features specific to AP workflows, teams are forced to manually complete a number of functions.

For example, vendor invoices must be manually entered and coded one-by-one, a slow and cumbersome process prone to data-entry errors. In addition, invoice approvals typically happen outside of QuickBooks, and usually must be manually tracked via email or chat or attached to the invoice after the fact.

After the invoice has been processed, the AP team queues up payments to suppliers, reconciles payments, and creates a QuickBooks payment record. Each payment type (i.e. check, credit card, or ACH) requires a separate workflow. Completing this tedious, multi-step process for each vendor invoice often takes several days — and sometimes weeks.

Improving the QuickBooks AP Workflow: 11 Reasons to Automate

While many organizations continue to rely on the current AP workflow in QuickBooks, the need for a more streamlined process is becoming increasingly clear. The good news is that the right AP automation solution can enhance efficiency, accuracy, and control over the AP process. By investing in an accounts payable software that is compatible with QuickBooks, teams can reap the following benefits:

Reduce Human Error

Manual data entry is a common source of errors in the AP process, from typos and incorrect entries to missed details. These seemingly minor oversights can lead to payment discrepancies, duplicate payments, delays, and potential financial losses. However, you can significantly reduce human error by automating invoice processing through an AP automation platform.

Capture Invoice Data More Accurately

MineralTree leverages advanced technologies like optical character recognition (OCR) coupled with human review to achieve high accuracy rates — over 99% on average — for invoice data capture. That means errors and duplicates are significantly less likely to slip through the cracks. Modern AP platforms, like MineralTree, also support multiple modes of invoice capture, such as header, or summary level capture as well as line detail capture, which helps further streamline your processes regardless of how your invoices are structured.

Keep Data Consistent With True Bidirectional Sync

With advanced automation tools like MineralTree, you don’t have to worry about data inconsistencies. Payments made within QuickBooks automatically sync with the AP automation software, and vice versa, which ensures accuracy across the board. With QuickBooks Online, MineralTree can also push captured invoice PDFs and additional documentation, ensuring the software retains all necessary records for digital archiving. For QuickBooks Desktop users, MineralTree even offers offline syncing via a connector that resides on the same server that Quickbooks is hosted on, allowing the two systems to sync even with Quickbooks offline.

Prolong the Lifespan of QuickBooks

Enterprise resource planning (ERP) system migrations tend to take upward of a year for planning, vendor selection, implementation, data migration and user training. It’s no surprise that they can be quite an expensive IT project requiring several dedicated resources. With the right automation solution, you gain enhanced AP functionality without requiring this time-consuming process.

Use the Same Automation Platform During an ERP Migration

If and when you do decide to migrate to a new ERP system, using the same automation platform before and after migration allows for seamless access to old invoices and data. As a result, it’s important to select a platform that can support multiple ERPs as you consider future needs. MineralTree also provides exceptional service and support, which is important to consider prior to any migration project. This helps ensure continuity in business operations and can facilitate a smoother transition with minimal data loss or disruption. It also helps reduce the learning curve associated with adopting a new automation solution.

Forge Biologics, a gene therapy company, invested in MineralTree to streamline their processes. MineralTree’s ability to integrate with multiple ERPs was a key benefit as they migrated away from QuickBooks. “We knew we’d eventually have to move to NetSuite,” said Steve Goden, SVP of Finance and Operations. “MineralTree offered proven APIs to both QuickBooks and NetSuite, so we knew we wouldn’t waste a lot of time and effort reconnecting the systems once we made the switch.”

Minimize Time-Consuming Work

Without automated bill capturing offered in QuickBooks, AP teams spend countless hours completing mundane and tedious tasks. Automation tools eliminate this manual work and streamline the entire AP process so you can pay vendors faster. Additionally, these tools provide the flexibility to set default coding fields, build allocation templates, and copy coding from previously posted invoices, further reducing manual efforts.

Add an Automated Approval Workflow

The lack of an integrated approval workflow and limited number of user licenses in QuickBooks often requires manual approvals via email. Automation solutions can improve the invoice approval workflow, by introducing automated processes that simplify and expedite the approval process, based on not only the vendor but also a number of dimensions.

With platforms like MineralTree, invoice approvals can all be done via email. Decision makers don’t even need to login into a complicated system and they can approve payments no matter where they are located. Reminders are also sent out automatically via the AP automation platform, so AP staff can reduce hours following up with department heads.

Leverage Analytics & Optimize Accounts Payable

QuickBooks offers a basic payment system but lacks advanced features such as scheduling payments or payment mix optimization. AP automation solutions enable you to optimize your payment mix and introduce strategic ePayment methods such as virtual cards.

By leveraging AP analytics tools and reports, companies can also determine how rebates and early payments can impact the bottom line. Simple Mills, a leading provider of better-for-you crackers, cookies, snack bars, and baking mixes, was able to use analytics tools from MineralTree to further improve their AP process. “We look at what could happen if we extend payment terms or ask for early-pay discounts with certain suppliers,” said Maddy McGannon, Simple Mills’ Controller. “MineralTree gives us the insight to analyze our payment data and use it to improve business decision making.” This contributes to cost savings and improves your cash flow management.

Eliminate Charges for Additional Users

QuickBooks charges on a per-user basis, which restricts scalability for growing businesses. MineralTree provides unlimited user access so you can scale without additional costs while maintaining user-defined roles to allow for segregation of duties

Pay Domestic and International Payments in the Same Platform

QuickBooks lacks integrated support for handling both domestic and international payments seamlessly. With the right automation solution, you can streamline workflows that handle both types of payments efficiently, eliminating the need for separate processes and platforms. Any additional reconciliation and journal entries required to balance transactions when purchasing foreign currency are automatically created by MinerlTree at the time of executing a foreign currency payment with the tool. As a result, companies can better streamline their payments in QuickBooks, while improving relationships with suppliers. .

Tailor for a Hybrid or Remote Workforce

QuickBooks Desktop lacks out-of-the-box support for hybrid or remote work setups, which can lead to inefficiencies for companies with multiple locations. By enabling remote access by default, cloud-based AP automation solutions can create a smooth AP workflow for hybrid or remote teams that eliminates travel time and improves overall efficiency.

The AP Workflow With QuickBooks and Automation

Finance professionals ranked AP as their top priority for digitization and automation in our 2022 State of AP Report — and for good reason. AP automation solutions offer comprehensive AP workflow capabilities that seamlessly integrate with QuickBooks. The workflow typically includes the following stages:

Invoice Capture

Automation tools provide advanced features for accurate invoice data capture. This includes the ability to create allocation templates for efficient coding and copying coding structures from previous bills.

Invoice Approvals

Automation solutions automate the invoice approval process based on specific conditions, eliminating manual intervention, centralizing and increasing visibility, and streamlining the workflow. Users can define customized criteria and parameters to automatically trigger the approval process for more efficient and consistent decision-making.

Payment Authorization

By centralizing payment authorization, you gain a secure platform for managing approvals. This doesn’t just improve efficiency, it also strengthens security measures for financial transactions.

Payment Execution

By integrating automation solutions with QuickBooks, you can initiate and process payments directly from the software interface, eliminating the need for manual data entry and enabling a streamlined, more efficient payment workflow. This integration saves time, minimizes errors, enhances financial accuracy, and provides a seamless experience for managing payments within the familiar QuickBooks environment.

Analytics and Reporting

AP automation solutions offer access to comprehensive analytics and reporting features that equip you with real-time insights into the AP process and payment status tracking. These robust analytics capabilities enable you to identify bottlenecks or delays, and make data-driven decisions to optimize your financial operations.

QuickBooks and AP Automation in Action: How Three Companies Improved Their Workflows

From quick service restaurant operators to dental service organizations and healthcare management companies, businesses across industries can reap the benefits of AP automation with QuickBooks. Let’s take a closer look at how these organizations improved their AP process.

MTB Increases Productivity by Combining Automation With Quickbooks

Montana Brand Management (MTB), a successful Taco Bell franchisee, faced a number of challenges with their manual, time-consuming AP process. Seeking a solution, they integrated MineralTree’s AP automation system with QuickBooks, resulting in near-instant process improvements.

With streamlined invoice management, enhanced payment security, and real-time visibility, MTB experienced a substantial reduction in AP processing time, improved vendor relationships, and increased focus on strategic business initiatives. The result? Higher productivity and increased operational efficiency.

Affinity Dental’s Explosive Growth Required a New Process in AP

Affinity Dental Management, a rapidly expanding dental service organization, was experiencing major challenges in managing their growing number of invoices and decentralized AP processes. Integrating MineralTree’s AP automation system with QuickBooks enabled streamlined invoice management, enhanced visibility, and the use of virtual cards for payments.

As a result, Affinity Dental improved efficiency, reduced manual data entry, and generated new revenue through cash-back rebates. The AP automation solution empowered the organization to better manage their business’s financial processes and support ongoing growth and excellence in dental services.

Cascade Senior Living Drives Efficiency Across its AP Function

Cascade Senior Living, a healthcare management company, faced multiple inefficiencies in their accounts payable (AP) processes, including a high volume of invoices and visibility issues due to remote locations.

After implementing MineralTree’s end-to-end AP automation solution, Cascade centralized their AP processes, increased efficiency, and reduced costs. The finance team experienced smoother workflows, improved accuracy, and greater ease of use, allowing them to focus on resident care while achieving a quick return on investment.


The basic AP functionality in QuickBooks can no longer drive the efficiency and accuracy most growing organizations require in today’s AP environment. However, the right automation solution enhances your AP workflow by providing advanced features and seamless integration. With automated AP processes, you can reduce human error, capture invoice data accurately, streamline approvals, optimize payment methods, and increase visibility through analytics and reporting. As a result, you can maximize the capabilities of QuickBooks and boost efficiency in your financial operations.

Request a demo today to learn more about how MineralTree can automate and streamline your accounts payable workflows in QuickBooks.

State of AP Report 2022 Download

Frequently Asked Questions

How do you track accounts payable in QuickBooks?

By clicking on Reports and scrolling down to “What You Owe”, you can run an Accounts Payable Aging Summary report and see total balances for current and late payments. By clicking on Expenses, you can drill down to get a more comprehensive overview of the money owed to vendors. However, AP automation tools make it easier to gain a deeper insight into your accounts payable through comprehensive reporting and more visibility into the process prior to posting invoices.

Does QuickBooks have automated workflows?

While QuickBooks does offer limited automation for certain types of bills, AP teams will reap more benefits from their ERP by leveraging an end-to-end AP automation solution that can integrate with this tool. ERPs are designed to cover a variety of business needs, which doesn’t always allow them to specialize as deeply in one function. As a result, AP automation tools can give teams the ability to better streamline their processes.

What can I automate in QuickBooks?

QuickBooks can automate several financial tasks, including recurring bills in AP and overdue payment reminders in AR. However, in order for teams to fully achieve an end-to-end AP automation process, they will need to invest in an automation tool, specifically designed to fit their needs.


We're transforming accounting by automating Accounts Payable and B2B Payments for mid-sized companies. Our award-winning solution has helped over one thousand businesses transform accounts payable from a source of inefficiency and fraud risk to a secure and strategic profit center that provides visibility into key cost drivers.