Manufacturing, warehousing, and distribution businesses rarely have simple payment workflows. A quote turns into an order. An order may require a deposit, staged billing, delivery confirmation, or recurring invoices. Then the payment has to match the right invoice and sync back to QuickBooks.
Method Pay was built to simplify that process by bringing payment collection into Method CRM, so teams can manage quotes, invoices, payments, customer records, and QuickBooks sync from one connected workflow.
TL;DR
- Method Pay is Method’s built-in payment processing for U.S. businesses using Method CRM with QuickBooks Online or Desktop, letting you collect card and ACH payments without a separate gateway.
- Every payment auto-matches its invoice and syncs to QuickBooks, replacing the three-system shuffle (invoice in Method, collect in a gateway, reconcile in QuickBooks) with one connected workflow.
- Manufacturers collect deposits before production and balance on completion; warehouses run recurring storage fees on autopay; distributors keep AR clean across hundreds of repeat accounts.
- Customers pay through a branded portal with your logo and no account required, via payment links attached to every invoice, with automated reminders handling follow-up.
- Keyed-in cards are included at the standard rate. Most B2B payments are keyed-in, not swiped, so the card-present rates other processors advertise rarely reflect what these businesses actually pay.
What is Method Pay?
Method Pay is Method’s built-in payment processing tool for businesses that use Method CRM and QuickBooks. Currently available to U.S. customers, it helps teams accomplish a number of things that directly benefit their businesses without logging into a separate gateway or re-entering data.
For example, they can:
- Collect card and ACH payments
- Send customers to a branded payment portal
- Match payments to invoices automatically
- Sync payment activity back to QuickBooks
Why payment workflows are harder for manufacturing, warehousing, and distribution businesses
Orders often start before the invoice exists
Long before an invoice reaches the customer, there’s already been plenty of work. Quotes or estimates are prepared, pricing is negotiated, purchase orders are approved, and sales orders are confirmed. In many cases, a deposit is collected before production begins, with the final invoice going out only after shipment or project completion.
Customers pay by invoice, phone, portal, or repeat billing, not by card in person
Manufacturers, warehouses, and distributors collect most payments through invoice links, over the phone, or through a portal after the job is done. These are keyed-in, card-not-present transactions, and that distinction matters when evaluating processing costs. Card networks price by fraud risk, and transactions where the card isn’t physically present carry higher interchange rates. This means the headline rates processors advertise, typically based on in-person payments, understate what a B2B business actually pays per transaction.
Cost is only half the equation, though. Because most of these sales run on credit terms, timing is the other. According to Atradius’s 2025 Payment Practices Barometer, 43% of U.S. B2B sales made on credit terms are overdue, driven largely by customer cash flow pressures — a problem compounded by manual follow-up across disconnected systems.
Reconciliation becomes harder as order volume grows
The bottleneck in B2B payment workflows is rarely collecting the payment. Rather, it’s knowing which invoice the payment belongs to and whether QuickBooks has been updated. The Federal Reserve has identified this as a common problem: retrieving remittance information remains a largely manual process, and in a Fed survey of over 2,000 businesses, more than 80% of small and mid-sized firms rated the ability to post and reconcile payments immediately as important.
How Method Pay connects quote-to-cash in one workflow
Create the quote or invoice in Method, then collect payment without switching systems
Method Pay’s payment workflow starts inside Method, where sales and customer work already happen. Teams can create quotes, convert them to invoices, collect payments, and sync everything to QuickBooks without switching systems. Workflow automation handles the handoffs between each step.
Let customers pay through a branded portal that looks like your business
Method Pay includes a branded payment portal where customers pay using card or ACH. Businesses can send payment links attached to individual invoices, collect deposits before work begins, and set up recurring billing for ongoing accounts.
Automatically match payments to invoices and skip the manual reconciliation
Every payment collected through Method Pay automatically matches its invoice and posts to QuickBooks the moment it lands. There’s no manual matching step and no cross-referencing a gateway report against a QuickBooks ledger.
Pro Tip: Automatically matching customer payments to invoices does more than save time, it reduces reconciliation errors that can delay month-end close and distort accounts receivable. Fewer unmatched payments also make it easier to identify outstanding balances and maintain accurate financial reporting.
Sync payment activity back to both QuickBooks Online and QuickBooks Desktop
Method Pay works with both QuickBooks Online and QuickBooks Desktop. Payments sync automatically and match the right invoice in both versions. According to Method’s own data, 86% of manufacturing, warehousing, and distribution prospects run QuickBooks only or QuickBooks plus spreadsheets, making a clean, direct QuickBooks sync essential.
What changes for manufacturers?
Taking deposits before production starts: How Method Pay handles upfront payments
Custom orders, made-to-order products, and large material purchases require upfront commitment before production begins. Method Pay supports deposit collection directly through the payment portal, so a manufacturer can send a deposit payment link as soon as the order is confirmed. It syncs to QuickBooks automatically, with no separate entry required.
Balance due when the job is complete: Collecting final payments without manual follow-up
Once production is done and delivery confirmed, the outstanding balance goes out as a second payment link, tied to the same customer and order record in Method. Automated reminders handle follow-up automatically. This staged billing approach, deposit first and balance on completion, is built into Method Pay.
Fewer handoffs between sales, production, and accounting
Customer status, order progress, payment receipt, and QuickBooks sync all stay connected in one place, so sales, production, and accounting share the same picture without checking separate systems.
What changes for warehousing businesses?
Recurring invoices and autopay for storage fees and repeat service charges
Warehousing businesses often bill recurring charges: storage fees, handling fees, monthly service agreements, and account-based recurring orders. Method Pay supports recurring invoicing and autopay through the Proposals App, so these charges run on schedule and post to QuickBooks automatically without manual intervention.
Payment status tied to the customer record before you release inventory
A warehouse team needs to know whether an account is current before releasing inventory or processing another order. When payment status lives in a separate gateway, that check means logging into another system. With Method Pay, it is visible directly on the customer record in Method.
Less manual follow-up on overdue invoices
Method Pay includes automated payment reminders that follow up on late invoices without manual intervention. Atradius reports that 5% of long-overdue US B2B invoices ultimately become bad debts; automated reminders reduce the manual follow-up load (and the write-off risk) as the customer base grows.
What changes for distributors?
Easier payment collection across a high volume of repeat customers
Distributors often manage hundreds of recurring buyers with open invoices running simultaneously. Method Pay keeps payment collection tied to each customer account, so every payment link, invoice, and payment record connects back to the right customer in Method and QuickBooks. Payment history for each account is visible in one place, simplifying AR review.
A branded payment portal that lets customers pay without creating an account
Method Pay’s payment portal lets customers pay by card or ACH without creating an account. They receive a payment link, click through to the branded portal, and pay. No registration is required, and the experience carries the business’s brand throughout.
Cleaner QuickBooks records across high invoice volume
When invoice volume is high, even a small mismatch rate creates a significant manual cleanup problem at month-end. Method Pay automatically matches each payment to the right invoice, reducing that cleanup to near zero. The warehousing and distribution workflow stays clean because the payment data never has to leave Method.
Why keyed-in card rates matter for manufacturing, warehousing, and distribution businesses
Most B2B payments in these industries aren’t swipe or tap transactions
Manufacturers, warehouses, and distributors collect most payments through invoice links, portals, or phone orders, which means they are keyed-in transactions rather than card-present swipes. Most processors advertise card-present rates, so businesses that primarily take keyed-in payments often pay more than the headline rate suggests. The Association of Financial Professionals’ 2025 Digital Payments Survey confirms that B2B payments run overwhelmingly on remote channels, not in-person card transactions, which is why the card-present rates processors advertise rarely reflect what a B2B business actually pays.
Method Pay includes keyed-in cards at its standard published rate
Method Pay offers a keyed-in card rate advantage, with no monthly minimums, no setup fees, and no gateway fees. Visit our Method Pay page for the latest rates.
Pro Tip: When comparing payment processors, don’t focus only on transaction rates. Consider the total cost of payment collection, including staff time spent reconciling payments, correcting posting errors, and following up on outstanding invoices. Automation can reduce these administrative costs significantly.
How the branded portal improves the customer payment experience
Customers pay through your brand, not a generic processor page
With Method Pay, customers pay through a branded portal that looks and feels like your business. Instead of landing on a third party payment page, they see your logo, your colors, and your brand.
Payment links on every invoice reduce back-and-forth after invoices are sent
Every invoice sent through Method can include a payment link that takes the customer to the branded portal. Customers click, review, and pay; an account login is not required. That one step replaces the follow-up emails and phone calls most AR teams deal with per invoice.
Deposits, staged billing, and recurring payments fit directly into operational workflows
The portal handles deposits, staged billing, and recurring payments, each tied to the customer record in Method and QuickBooks, whether that’s a deposit before production, a balance after fulfillment, or recurring storage fees on autopay.
Fee passthrough can help offset processing costs for eligible businesses
For eligible businesses, Method Pay supports fee passthrough, shifting the processing fee to the customer so the business nets the full invoice amount. Surcharge rules vary by state, so confirm what is allowed before enabling it.
How Method Pay reduces reconciliation work in QuickBooks
The old way: Create the invoice, collect the payment, then manually update QuickBooks
Before Method Pay, a typical Method and QuickBooks user followed three steps for every transaction: create the invoice in Method, log into a separate gateway to collect payment, then go back to QuickBooks to match it and close the invoice.
The Method Pay way: Invoice, collect, and sync in one place
Method Pay collapses that process into one. The invoice lives in Method. The customer pays through the Method portal. The payment auto-matches its invoice and syncs to QuickBooks instantly, with no manual entry. Fees, refunds, and chargebacks are managed from the same dashboard.
Month-end gets cleaner when payments auto-match every time
The speed advantage with Method Pay is how fast the books close. When every payment auto-matches its invoice and syncs to QuickBooks, month-end reconciliation shrinks to a quick review. Method’s internal data shows that 82% of manufacturing and distribution prospects cite order management pain as a primary challenge. Manual reconciliation is a core driver of this.
Who is Method Pay best suited for?
Method Pay works best for:
- U.S.-based businesses using Method CRM
- Businesses using QuickBooks Online or QuickBooks Desktop
- Manufacturers, warehouse businesses, and distributors that invoice customers
- Teams that collect deposits, staged payments, or recurring payments
- Businesses that want customer records, invoices, payments, and QuickBooks sync in one connected system
Method Pay feature summary
| Feature | Why it matters for manufacturing, warehousing, and distribution |
|---|---|
| Quote-to-invoice workflow | Keeps payment collection connected to the original customer request |
| Branded payment portal | Gives customers a professional place to pay online |
| Payment links | Reduces manual back-and-forth after invoices are sent |
| Deposits | Helps collect money before production, delivery, or service begins |
| Staged billing | Supports progress payments and balance-on-completion workflows |
| Recurring billing | Useful for repeat service, storage, and account-based billing |
| Automated reminders | Helps reduce manual AR follow-up |
| QuickBooks sync | Updates accounting records without double entry |
| Auto-matching | Reduces reconciliation work and month-end cleanup |
| Cards and ACH | Supports common B2B payment methods |
FAQs about Method Pay for manufacturing, warehousing, and distribution
Method Pay is Method’s built-in payment processing tool. It lets businesses accept card and ACH payments, send branded payment links, collect deposits, set up recurring billing, and sync payments to QuickBooks automatically, without using a separate payment gateway.
Method Pay helps manufacturers collect deposits, send invoices, accept payments online, and sync everything to QuickBooks without a separate payment system. Deposit, staged, and balance-on-completion workflows all run from the same customer record in Method.
Method Pay helps distributors tie payment links, invoices, customer records, and QuickBooks sync together in Method. Every payment auto-matches its invoice, keeping AR records clean across high invoice volumes.
Method Pay supports recurring billing, automated reminders, and payment tracking, helping warehousing businesses manage storage fees and repeat customer billing without manual follow-up.
Yes. Method Pay works with both QuickBooks Online and QuickBooks Desktop. Payments sync to QuickBooks and automatically match the correct invoice in both versions.
Yes. Customers can pay invoices through a branded portal by card or ACH without creating an account. Every invoice can include a direct payment link.
Yes. Method Pay supports deposits, staged billing, recurring billing, and autopay. More complex workflows may require customization.
Not presently. Method Pay is currently available only to U.S.-based businesses.
Payments should stay connected to the customer workflow
Manufacturing, warehousing, and distribution businesses need more than a way to accept payments. They need payments connected to quotes, invoices, customer records, and QuickBooks, without the manual work that builds up when those systems are separate.
Method Pay brings that into Method. Explore Method Pay or book a demo to see how it fits your workflow.
