How to Enable Invoice or Pay Later Checkout in Shopify [2025]

Many online businesses, including B2B companies, government agencies, educational institutions, and large wholesale buyers, often ask, “Can we check out now and pay later by invoice?” This inquiry relates to a popular B2B payment option known as invoice payment, “Net Payment Terms,” or “Pay Later” checkout in Shopify.

While Shopify doesn’t offer a direct invoice-based checkout right out of the box, setting it up is a breeze with its built-in features. With a few smart tweaks to your workflow and some helpful app integrations, you can have it running smoothly in no time.

In order to improve your B2B eCommerce capabilities, this guide will give you a clear, step-by-step process for enabling invoice payments (such as Net 30, Net 60) directly within your Shopify store.

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Understanding Net Terms or Pay Later Checkout in Shopify

The Net Terms or Pay Later checkout in Shopify option fundamentally changes the point of payment in a transaction:

• Order Submission: Without making an immediate payment, your customer completes the checkout process by placing an order, frequently accompanied by a Purchase Order (PO) number.
• Shipping & Fulfillment: As the merchant, you carry on with the order’s normal shipping and fulfillment.
• Deferred Payment: The invoice is paid by the client within a predetermined window of time, usually 30 (Net 30), 45 (Net 45), or 60 (Net 60) days after the invoice date.

For serving wholesale distributors, buyers, institutions, and established corporate accounts that normally function on credit terms rather than immediate credit card payments, this trade credit approach is absolutely necessary.

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Who Benefits from Pay Later Checkout in Shopify?

This payment flexibility is crucial for:

• For wholesale/b2b buyers, such as distributors, resellers, and other large buyers who must receive goods before payment, this payment flexibility is essential.
• Non-profits and government agencies are businesses with particular procurement procedures that depend on invoice-based payments.
• Companies with established credit lines or procurement departments that handle payments centrally are considered approved corporate accounts.
• Loyal business-to-business clients with whom you have pre-approved credit terms are known as existing trusted customers.
• Educational Institutions: Purchase order systems are frequently needed by colleges, universities, libraries, and schools.

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How to Set Up Pay Later Checkout in Shopify (Without Shopify Plus)

Follow these simple, actionable steps to enable invoice payment options in your Shopify store:

Step 1: Enable a Custom Manual Payment Method (“Invoice” or “Net Terms”)

Shopify provides the necessary infrastructure for manual payments.

1. Access Payment Settings: In your Shopify Admin, navigate to Settings → Payments
   
   
   
2. Add Manual Method: Under the “Manual payment methods” section, click “Add manual payment method.”
   
   
   
   
3. Name It Clearly: Give your method a descriptive and professional name that B2B customers will understand, such as:
   • Invoice (Net 30)
   • Pay by Purchase Order
   • Wire Transfer (Approved Accounts Only)
     
     
     
4. Provide Instructions: Crucially, add clear payment instructions. This is where you communicate the terms and eligibility:
   • “This option is only available for approved business accounts and wholesale partners.”
   • “An invoice will be emailed to your registered account after checkout, payable within 30 days.”
   • “Please ensure your Purchase Order (PO) number (if applicable) is entered in the order notes field.”
     
5. Visibility: Customers will now see this payment option alongside traditional credit card or digital wallet options at checkout.

Step 2: Control Who Can Use Invoice Payment (Customer Segmentation)

To keep all customers from using invoice terms, we need to put a solid control system in place:

1. Use Shopify Customer Tags (Primary Method): This is the most effective and scalable way to manage eligibility.

Here, you can pre-approve customers (e.g., via a B2B registration form) and tag their Shopify accounts with specific indicators, such as:

• net-30-eligible
• invoice-approved
• wholesale-partner

• While Shopify’s native manual payment methods DON’T hide based on tags, you can (and should) clearly state in the instructions (from Step 1) that this option is only for approved, tagged customers. You would then manually review orders placed via this method by untagged customers and follow up as necessary.
  
• For stricter control: On Shopify Plus, you can use Shopify Scripts to hide/show payment gateways based on customer tags dynamically. For other Shopify plans, you can use a B2B lock app for Shopify, such as Wholesale Lock Manager: B2B, which may allow you to restrict access to your B2B payment gateway page. OR you can also manage all your processes of buy now, pay later checkout in Shopify with the Wholesale Pricing Discount B2B app. This app offers a net payment terms checkout like Net30, Net60, Net90, where Shopify merchants can customize it for each customer type (based on tags).

2. Clear Communication: It is also important to make sure that your B2B signup page, wholesale terms and conditions, and pre-checkout information clearly state the requirements for using this pay-later (invoice) payment option.

Step 3: Collect Purchase Order (PO) Numbers (Recommended for B2B)

Purchase Order numbers are vital for B2B tracking and reconciliation. Here are the things you might need to implement.

• Shopify’s Cart Notes: Enable the “cart notes” field in your theme settings, and instruct customers to input their PO number here. This is simple and built-in.
  
• Additional Checkout Fields (Via Apps): For a more structured approach, use a Shopify app designed to add custom fields to the checkout process. Search the Shopify App Store for “PO Number,” “Order Notes,” or “Custom Fields at Checkout” apps. These allow for dedicated input fields that appear clearly during checkout.

Step 4: Create and Send Invoices, and Track Payments

Once an invoice-based order is placed, your workflow shifts to fulfillment and Accounts Receivable.

1. Order Status in Shopify: Shopify will automatically create an “unpaid” order in your admin dashboard.
2. Invoice Generation:
   • Manually: Generate a formal invoice using your preferred accounting software (e.g., QuickBooks, Xero, FreshBooks, Zoho Books). You’ll typically pull the order details from Shopify and input them into your accounting system.
   • Automated Integration: Implement direct integrations between Shopify and your accounting software. Many modern accounting platforms offer native Shopify connectors, or you can use integration tools like Zapier to automate order syncing and invoice creation.
   • You can also choose Shopify invoice creator apps – available on the App Store.
3. Send Invoice: Email the formal invoice to your customer’s billing contact.
4. Mark Order Paid: Once you receive payment (via bank transfer, check, etc.), manually mark the order as “paid” in your Shopify admin. This updates your order status and financial records.
5. AReceivables (Recommended App): For managing unpaid b2b invoices, sending automated payment reminders, tracking balances, and simplifying your Accounts Receivable workflow, a dedicated app like AReceivables is invaluable. This tool helps you maintain healthy cash flow and ensures timely payments.

Real-World Example of Implementing Pay Later Checkout in Shopify 

Business: A leading provider of Commercial Office Supplies to businesses and institutions globally.

• Customer: A local government department (pre-approved and tagged net-30-approved in Shopify).
• Ordering Process: The department’s procurement officer browses the online catalog on the Shopify store. They add needed supplies to their cart and proceed to checkout.
• Payment Selection: At the payment step, they select “Invoice (Net 30)” from the available options.
• PO Number Input: They enter their internal Purchase Order number in the designated checkout field (added via a custom fields app).
• Order Placement: The order is placed in Shopify as “unpaid.”
• Invoice & Fulfillment: The commercial office supplies company receives the order, automatically syncs it to their QuickBooks account (via integration), which then auto-generates a formal invoice. The order is then fulfilled and shipped.
• Payment & Reconciliation: The local government department pays the invoice via bank transfer within 30 days. The company’s finance team then marks the order as “paid” in Shopify and QuickBooks, completing the transaction cycle.

This entire, streamlined flow for B2B payment terms is managed effectively within a standard Shopify setup, without the need for Shopify Plus or complex custom coding.

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Recommended Apps (Optional, but Highly Recommended for Efficiency)

Purpose	Recommended Tool(s)	Benefit
Invoice payment option at checkout	Shopify Manual Payments (built-in)	Core functionality; no app needed for basic option.
Invoice automation & accounting	QuickBooks, Xero, FreshBooks, Zoho Books	Automate formal invoice generation, manage ledgers, simplify financial reporting.
Invoice reminders and management	AReceivables	Automate payment reminders, track balances, streamline Accounts Receivable workflow for B2B.
Bulk ordering for wholesale buyers	WSH Order Form & ReOrder	Enhance B2B ordering experience with fast, multi-SKU selection.
Customer tagging & workflow automation	Shopify Flow (Advanced/Plus) or automation apps	Automate approval workflows, customer tagging, and internal notifications for B2B leads.
Custom checkout fields (for PO numbers)	Shopify App Store: “PO Number” or “Custom Fields” apps	Add dedicated fields at checkout for collecting crucial B2B order information like PO numbers.

Final Summary: Successfully Enable Pay Later Checkout in Shopify

Providing invoice or Pay Later Checkout in a Shopify store is essential to efficiently catering to your institutional, B2B, and wholesale clients. It’s an easy process that doesn’t require sophisticated coding or Shopify Plus.

All you need is a strategic combination of:

• A well-defined manual payment method (e.g., “Invoice (Net 30)”).
• Clear customer segmentation (via tags) and communication to control eligibility.
• Optional, but highly recommended, integration with robust accounting software and Accounts Receivable management apps for streamlined invoicing and tracking.

This powerful setup allows you to provide essential B2B credit terms, significantly improving the purchasing experience for your high-value business clients, fostering loyalty, and expanding your market reach.

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Frequently Asked Questions (FAQs) About Invoice, Net Terms, and Pay Later Checkout in Shopify

These FAQs address common queries regarding enabling Pay Later checkout in Shopify.