Both QuickBooks Desktop and QuickBooks Online have Accounts payable automation capabilities. However, the AP automation capabilities are limited to uploading bills and paying the bills. There is no approval workflow and invoice capture capabilities that you would find in an AP automation tool.

If you are struggling with end-to-end payable workflow, you might want to upgrade your accounting software to an expensive ERP solution. But there is a simple solution: you can use an Accounts payable software that provides seamless integration with QuickBooks (Desktop and Online version)

Managing accounts payable in QuickBooks could lead to the following challenges:

1. Manually matching invoices with purchase orders and receipts.
2. Chasing employees to get invoices approved on time and close the books.
3. Lacking real-time visibility into invoice approval and accounts payable.
4. Running out of QuickBooks user licenses.
5. You are providing all employees with access to your accounting system, and if access control is not in place, someone can easily mess up the books.

You can implement an accounts payable automation software that works with QuickBooks and extends the functionality of QuickBooks.

We will present how ProcureDesk’s cloud-based solution helps automate the accounts payable process in QuickBooks. We will cover the key functionality needed to automate your accounts payable process. 

ProcureDesk supports both QuickBooks online accounts and QuickBooks Desktop or QuickBooks Enterprise.

If you want to see how ProcureDesk can help you with AP automation and reduce the invoice processing time by up to 40% click here to schedule a free demo.

Let’s look at the complete functionality of the accounts payable solution.

Accounts Payable Automation Steps

Automating accounts payable (AP) for QuickBooks streamlines invoice processing improves accuracy, and enhances financial control. Here’s a step-by-step breakdown of how AP automation works with QuickBooks using a solution like ProcureDesk:

1. Invoice Capture – Invoices are automatically extracted using OCR, eliminating manual data entry. This reduces the manual errors in data entry and streamlines invoice management.
2. Three-Way Matching – Invoices are matched with POs and receipts, flagging discrepancies.
3. Automated Approvals – Invoices route through predefined approval workflows, reducing delays.
4. QuickBooks Integration – Approved invoices sync with QuickBooks, ensuring real-time financial tracking.
5. Payment Processing – Payments are scheduled via ACH, checks, or virtual cards, improving efficiency.
6. Reporting & Audit – Dashboards provide spend visibility, tracking vendor payments and compliance.

Step 1: Automate The Invoice Capture Process

Manual data entry of invoices consumes time and leads to human error. By automating the invoice capture process, you can free up time for your AP team and streamline the AP process.

There are multiple ways to automate the invoice capture process in ProcureDesk.

Creating invoices from your AP inbox:

You can import invoices directly from an email to simplify your bookkeeping process. Here are the exact steps for that:

• Set Up an AP Email – Use a dedicated or general-purpose AP email for receiving invoices.
• Enable Auto-Forwarding – Automatically forward invoices from your AP email to the ProcureDesk system.
• Import Invoices – The system captures and processes invoices directly from your email.
• Scan & Forward Paper Invoices – Scan paper invoices and email them to the same AP address for seamless processing.

There are two other alternative approaches for importing invoices into the system:

1. Vendor invoices can also be submitted using a supplier portal. This can be managed during the supplier onboarding process.
2. You can use cXMl or EDI tools to import invoices into the system.

Step 2: Automated Invoice Matching And Coding

After an invoice is imported into the system, it runs it through an OCR (Optical Character Reader) process.

The system uses OCR and AI to capture invoice data and automatically create an invoice from it. There is no need to manually enter the invoice into the system, saving the AP team time and eliminating manual data entry errors.

After an invoice is imported, there are two ways to match and code the invoice.

If the purchase order number is provided on the invoice, the system automatically matches it with an existing purchase order and receipt if present.

A purchase order can be created in ProcureDesk, or the system can import it from QuickBooks. Purchase orders in a different system can be imported using a bulk upload process or leveraging the open APIs.

The system can perform a 3-way match or a 2-way match depending upon the type of the invoice. The system typically matches the following information:

1. Quantity received with ordered and invoiced quantity.
2. Order and invoice unit price.
3. Invoice total and the order total.

By automating the matching process, you will save time and ensure that you are only paying for fully approved invoices.

Invoices can be coded based on the following rules:

1. If the purchase order (PO) is present, the invoice can be automatically coded based on GL or other cost codes assigned to the PO.
2. If the purchase order is not present, the system can use inbuilt rules to assign coding based on the suppliers or similar previous purchases.

If the invoice doesn’t mention a purchase order number, you can send the invoice for approval using the approval workflow engine. This is called a non-PO invoice process.

Step 3: Automated Approval Workflows

Automated approval workflows in AP (Accounts Payable) workflow software streamline how invoices are routed for approvals, ensuring that exceptions are handled efficiently. When invoices don’t match purchase orders or non-PO invoices require approval, the software automatically routes invoices to the appropriate approvers based on predefined rules.

This AP workflow can be customized to reflect your organization’s hierarchy and approval policies. For example, if an invoice exceeds a certain amount or includes an exception, the system sends it to the designated manager for review. This automation reduces the back-and-forth of manual approvals, cuts down on delays, and ensures that invoices are approved promptly.

You can easily track what is approved and what is pending for approval using a dashboard:

Invoice Approval Workflow

By leveraging the automated workflows, you can see the following benefits:

• Faster Approvals: Automated workflows ensure invoices reach the right person quickly, speeding up the approval process and reducing bottlenecks.
• Enhanced Compliance: The software tracks each step of the approval process, ensuring that every invoice follows company policies and audit requirements.
• Early Payment Discounts: By expediting the approval process, companies are more likely to take advantage of early payment discounts offered by vendors. Paying invoices promptly can result in significant cost savings over time.

Automated approval workflows not only simplify invoice processing but also improve cash flow management by enabling companies to capitalize on early payment discounts.

Step 4: QuickBooks Integration

Once an invoice is approved in ProcureDesk, the system automatically syncs the bill directly with QuickBooks, so you never have to worry about manual data entry.

After the invoice is matched, coded, and approved in ProcureDesk, it’s automatically synced with your QuickBooks account.

The integration is real-time—no need to export or manually enter data. All relevant details, including vendor information, line items, amounts, and payment terms, are accurately transferred to QuickBooks without additional steps.

For QuickBooks Desktop, the integration can triggered on a desired frequency – for example every 15 minutes. 

Related: Accounts Payable Software Compatible With QuickBooks

Step 5: Supplier Onboarding and Payment Processing

ProcureDesk’s AP automation software takes the hassle out of manual data entry and endless follow-ups for the vendor setup process. ProcureDesk simplifies vendor onboarding with automated approval workflows, eliminating manual data entry and follow-ups. 

Automated Approval Workflows

Suppliers can enter their details through a secure portal, upload documents like W-9 forms and bank details, and agree to payment terms—all in one place.

ProcureDesk automatically routes the setup request to the relevant approvers. It automatically flags any missing documents or discrepancies. Approvers receive instant notifications and can review, approve, or request changes directly from their email or mobile device, keeping the process moving quickly. No more chasing down approvals—everything is tracked in real-time.

Why This Matters:

• Faster Onboarding: Automated workflows mean suppliers are approved and ready to work faster, so you can start processing invoices without delay.
• Accurate Data and Compliance: All supplier data is captured accurately the first time, ensuring you meet compliance standards with a full audit trail of approvals.
• Optimized Payment Terms: Quickly onboarding suppliers allows you to establish and agree on payment terms early, helping manage cash flow better.

Vendor payments

Once a supplier is approved, you can pay vendors directly through ProcureDesk or use QuickBooks for payments. ProcureDesk seamlessly syncs payment information back into the system, ensuring complete financial visibility.

Here is how you can track the payment details in ProcureDesk:

Step 6: Supplier Onboarding and Payment Processing

ProcureDesk provides real-time dashboards that offer complete spend visibility, tracking vendor payments, invoice approvals, and compliance. Finance teams and management can monitor cash flow, analyze spending trends, and ensure adherence to budget policies.

For auditors, the system maintains a detailed audit trail of every transaction, capturing approvals, edits, and payment records. This ensures compliance with internal controls and simplifies audits by providing easy access to historical financial data—all in one centralized platform.

Here is how you gain better spend visibility with ProcureDesk:

How Does ProcureDesk Integrate With QuickBooks?

ProcureDesk seamlessly integrates with QuickBooks, giving you the flexibility to manage vendor payments using QuickBooks’ native payment capabilities or using inbuilt system capabilities. Once invoices are approved and synced to QuickBooks, you can leverage QuickBooks’ payment process to handle vendor payments directly.

QuickBooks offers multiple payment methods, including ACH transfers, credit card payments, and issuing paper checks. After ProcureDesk syncs approved bills to QuickBooks, you can initiate payments using your preferred method. QuickBooks manages the vendor payment process, making it easy to pay vendors on time and keep your payment workflows consistent.

After processing payments in QuickBooks, the payment data is automatically synced back to ProcureDesk. This includes payment status, details, and confirmation, providing full visibility into the payment process within ProcureDesk. This two-way sync eliminates the need for manual updates and ensures your records remain accurate and up-to-date.

Key Benefits:

• Streamlined Payment Process: Easily manage payments directly in QuickBooks using familiar tools and processes.
• Full Visibility: Payment information syncs back to ProcureDesk, keeping your AP records complete without additional manual input.
• Flexibility: Choose the best vendor payment method, from ACH to paper checks, based on your business needs.

Related: Accounts Payable Automation For QuickBooks

Integration With QuickBooks Online

AP automation software integrates seamlessly with QuickBooks Online and QuickBooks Online Advanced, ensuring a smooth, real-time connection between your procurement and accounting systems. This integration simplifies the management of master data, automates data sync, and enhances overall efficiency in your AP workflow.

With ProcureDesk’s AP automation software, your master data—such as GL accounts, suppliers, and payment terms—are automatically synced with QuickBooks Online. This ensures consistency across systems, reducing manual data entry and minimizing errors. Any updates to GL accounts, supplier details, or payment terms made in QuickBooks are reflected instantly, keeping your systems aligned.

The two-way sync feature keeps supplier and item information accurate and up-to-date between both systems. Add or update a supplier in QuickBooks, and those changes sync automatically with the AP automation system, and vice versa. This streamlines supplier management, eliminating the need for separate records across platforms.

A key benefit of this integration is the real-time sync for purchase orders and bills. When a purchase order is created in the AP automation system, it syncs instantly with QuickBooks, ensuring your financial data is always current. Approved bills are also immediately available in QuickBooks, ready for payment processing without delay.

Integration With QuickBooks Desktop

Our AP automation software integrates with QuickBooks Online, QuickBooks Desktop, or QuickBooks Enterprise. The Intuit QuickBooks Desktop version has many variations, and our systems support all these versions.

The integration with the Desktop version has similar capabilities as the online, including the two-way sync for suppliers and items.

The integration process is the same, except that integration with QuickBooks Desktop is supported through QuickBooks web connector. The integration is not real-time as QuickBooks Online but you can setup the web connector to run every 5-10 mins to keep it close to real-time integration.

Frequently Asked Questions (FAQs):

Can Accounts Payable Be Automated?

Yes, accounts payable can be automated using AP automation software. Automation streamlines invoice processing, data capture, approval workflows, and payments, reducing manual effort, errors, and processing time. This helps improve accuracy, enhances efficiency, and allows your team to focus on more strategic tasks.

Does QuickBooks Online Have AP automation?

QuickBooks Online has basic AP automation features, such as invoice tracking, bill payments, and vendor management. However, for more advanced AP automation—like automated invoice data capture, approval workflows, and real-time syncing with other systems—integrating with specialized AP automation software provides a more robust solution.

What Is The Accounts Payable Process?

The accounts payable (AP) process involves managing a company’s short-term debts or obligations to suppliers. It typically includes the following steps:

1. Invoice Receipt: Collecting invoices from suppliers.
2. Data Capture: Extracting invoice details like amounts, dates, and vendor information.
3. Invoice Matching: Comparing invoices with purchase orders and receipts to ensure accuracy.
4. Approval Workflow: Routing invoices for approval based on company policies.
5. Payment Processing: Scheduling and making payments to vendors via checks, ACH, or other methods.
6. Record Keeping: Updating accounting records to reflect payments and maintain compliance.

Automating these steps enhances efficiency, accuracy, and control.

Does ProcureDesk Support QuickBooks Desktop Taxes?

Yes, ProcureDesk supports QuickBooks Desktop taxes. The integration ensures that invoice tax information is accurately captured and synced with QuickBooks Desktop, maintaining consistency in your financial records.

What Is The Pricing Of ProcureDesk AP Automation Software?

ProcureDesk’s AP automation software pricing varies based on factors such as the number of users, the volume of invoices processed, and the specific features required by your business. You can check the latest pricing here.

Which Versions Of QuickBooks Desktop Does ProcureDesk Support?

ProcureDesk supports multiple versions of QuickBooks Desktop used by small business, including but not limited to:

• QuickBooks Pro
• QuickBooks Premier
• QuickBooks Enterprise

What Are The Benefits Of Accounts Payable Automation?

1. Time Savings: Automation eliminates manual data entry and processing, speeding up invoice approvals and payments.
2. Error Reduction: Automated data capture minimizes human errors, ensuring accurate invoice processing and fewer discrepancies.
3. Faster Approvals: Streamlined approval workflows reduce bottlenecks, allowing invoices to be approved and paid promptly.
4. Cost Efficiency: Reduces operational costs by lowering manual work, avoiding late fees, and capturing early payment discounts.
5. Enhanced Visibility: Real-time tracking and reporting provide better insights into cash flow, helping with financial planning and decision-making.

How Does Accounts Payable Automation Streamline Invoice Processing?

AP automation solution streamlines invoice processing by automating key steps like data capture, invoice matching, and approvals. Invoices are quickly scanned using OCR, matched against purchase orders, and routed through automated approval workflows, reducing manual effort and errors.

The system provides real-time updates and integrates with accounting software like QuickBooks, ensuring accurate and timely processing. This efficiency speeds up payments and improves cash flow management by reducing delays and allowing better control over outgoing funds.