Integration · QuickBooks Enterprise · 6 enterprise industry editions · SDK · 48-hour go-live
Clarity Payment Hub™/Integration

QuickBooks Enterprise + Payment Hub, invoice and deposit payments recorded in QuickBooks through the Desktop SDK

Card and ACH payments from invoice links, a customer portal and the office that land in QuickBooks Enterprise as ReceivePayment transactions, applied to the right invoice, without re-keying.

6
Enterprise
Industry Editions
SDK
qbXML · Web
Connector
19+
Gateways
Supported
11
Payment Hub
Use Cases
48hr
Go-Live
Timeline

Why QuickBooks Enterprise businesses add Payment Hub, and what changes when they do

QuickBooks Enterprise is the point where a growing business has outgrown Pro and Premier but is not ready for a full ERP. It handles more users, more list entries and more inventory. Taking and recording payments is still mostly a manual job, and the volume that pushed you to Enterprise is the same volume that makes it painful.

The businesses we see on Enterprise share a pattern. Invoices go out by email from QuickBooks. Some customers mail checks. Some call with a card, which someone types into QuickBooks Payments or a separate terminal. A few set up their own ACH. At the end of the week the bookkeeper opens the merchant portal and the bank feed and works out which payment belongs to which invoice, then records ReceivePayment transactions one at a time. Deposits get matched in the bank feed if the amounts line up and chased if they do not.

Payment Hub takes that apart. The customer pays from a link on the invoice QuickBooks already sends, or in a portal that shows their open invoices, and the payment is written into QuickBooks as a ReceivePayment applied to that invoice, into Undeposited Funds or straight to the bank account, the way your books are set up. The bookkeeper reviews a list of applied payments instead of building it.

The reason this matters at Enterprise scale is that the bookkeeper is often the whole accounting department. A business doing 400 invoices a month with one person in the back office cannot afford a payment process that takes a day a week. Removing the re-keying is where that day comes back.

What stays in QuickBooks Enterprise

QuickBooks remains the system of record. Customers, items, invoices, sales orders, payments and the bank register all stay in your company file. Payment Hub reads customers and open invoices through the SDK and writes payments back in the same transaction types your bookkeeper would enter. Reports look the same, with fewer gaps.

Your existing Enterprise setup does not change. Invoice templates, payment terms, item lists, class tracking, Advanced Inventory and Advanced Pricing all stay as configured. Payment Hub adds a payment link to your invoice template and a portal beside QuickBooks, not inside it.

Clarity's role: Payment Hub is the payment-acceptance layer for QuickBooks Desktop Enterprise. Customer portal, payments recorded as ReceivePayment and Sales Receipt transactions, 19+ gateway choices, Level III on commercial cards, deposit and progress-billing handling and multi-file routing, all through the Desktop SDK and Web Connector. Your company files, templates and other integrations stay untouched.

QuickBooks Enterprise industry editions, all served by Payment Hub

Intuit ships Enterprise in industry editions that add features for specific kinds of business. Payment Hub works across all of them, and the payment pattern that matters most changes with the edition.

Industry Editions Supported
Contractor
Manufacturing
& Wholesale
Retail
Professional
Services
Nonprofit
Accountant
& General

Contractors on Enterprise live on deposits and progress billing, so the integration between sales orders, progress invoices and payments is the feature they notice. Manufacturing and wholesale businesses carry the most open invoices and get the most from the portal and consolidated payment. Professional services firms want retainers and scheduled draws. Retail businesses on Enterprise usually already have a point-of-sale system and use Payment Hub for invoiced and phone sales that the POS does not cover. Nonprofits use it for pledges and program fees that need to hit the right class.

Because the same Enterprise install often serves a business that fits two editions, the full feature set is installed and you enable what your office uses.

Payment Hub vs QuickBooks Payments, honest side-by-side

QuickBooks Payments is Intuit's own processing, built into Enterprise, and for a small business it is a sensible default. Payment Hub is the option for businesses that have outgrown it, and the differences are concrete.

CapabilityQuickBooks PaymentsPayment Hub on QuickBooks Enterprise
Gateway / processor choice✗ Intuit is the processor, at Intuit's rates✓ 19+ gateways on your merchant account: Worldpay, Adyen, Cybersource, Fortis, PayTrace, Stripe, Braintree, Authorize.Net and more
Customer self-service portal✗ Pay-now on an emailed invoice only, one invoice at a time✓ Branded portal showing all open invoices, pay-many, pay-on-account and saved methods
Click-to-pay links on invoices✓ Included on emailed invoices✓ Included, tokenized, on your invoice template, with the payment applied automatically
Level III line-item data✗ Not sent✓ Line detail from the invoice attached to eligible commercial card transactions
Deposits and progress billing✗ Manual application of a deposit to a later invoice✓ Sales order deposits and progress invoice payments apply automatically
Multi-company files✗ Separate Payments account per company file✓ One configuration mapping each company file to its merchant account and bank
ACH / eCheck✓ Included, with Intuit's ACH pricing✓ ACH, eCheck and card on one portal, at your bank's or gateway's rates
Recurring and scheduled payments✓ Recurring sales receipts✓ Scheduled draws, statement autopay and installments, with dunning on failed attempts

QuickBooks Payments is the right answer for a business with modest card volume that values having everything from Intuit. The case for Payment Hub starts when your processing fees become a line item you notice, when customers ask to pay several invoices at once, when you run more than one company file, or when deposits and progress billing turn into monthly cleanup. Any one of those is usually enough.

The Missing LinkBetween Paymentsand Your ERP

Clarity Payment Hub closes that gap, connecting your orders, invoices, and payment channels into one flow.

Speak to a Platform Architect

How Clarity Connect integrates Payment Hub with QuickBooks Enterprise

The integration uses the QuickBooks Desktop SDK with the QuickBooks Web Connector, Intuit's supported path for third-party applications on Enterprise. Eight capabilities make up the integration, and none of them modify your company file structure or require add-on code inside QuickBooks.

QuickBooks Desktop SDK integration

Payment Hub exchanges qbXML with QuickBooks Enterprise through the Web Connector: it reads Customers, Invoices, Sales Orders and Credit Memos, and writes ReceivePayment and Sales Receipt transactions. The Web Connector runs on your QuickBooks host and connects outbound on a schedule you set.

Payments recorded as QuickBooks transactions

A payment taken on an invoice link, in the portal or by phone is written to QuickBooks as a ReceivePayment applied to the invoice it settles, or as a Sales Receipt for a sale with no invoice, into Undeposited Funds or the bank account your books use.

Deposit and progress-billing aware

Deposits on sales orders, payments on progress invoices against an estimate and final balances are handled as separate transactions that apply correctly, so job-based businesses stop reconciling deposits by hand.

Level III auto-enrichment

Line detail from the invoice, including item, quantity, rate and tax, is attached to eligible commercial card transactions so they settle at Level III interchange. Most useful for wholesale and manufacturing customers selling to other businesses.

Multi-company file routing

Each company file is mapped to its own merchant account and bank account. Businesses that run several entities in separate files get one configuration and one portal login for customers who deal with more than one of them.

Tokenized method vault

Cards and bank accounts are tokenized at the gateway and stored against the QuickBooks customer, so saved-method payments and portal use never put card data in your company file or on your network.

Recurring and scheduled payments

Retainers, statement autopay and installment plans run on the scheduler, with dunning on failed attempts and every successful run recorded in QuickBooks as a normal ReceivePayment or Sales Receipt.

Compatible with hosted Enterprise and other integrations

Works with Enterprise on-premise and on hosting providers such as Right Networks, and alongside other Web Connector applications you already run. It does not replace them and does not compete for the company file.

The integration workflow, sales order deposit to reconciled bank deposit

A concrete walk-through. A commercial HVAC contractor on QuickBooks Enterprise Contractor Edition, hosted on Right Networks, wins a $37,900 rooftop unit replacement that requires a 50 percent deposit before equipment is ordered. Payment Hub handles the deposit, the final invoice and the bank deposit, through the Desktop SDK.

01

Estimate converts to a sales order in QuickBooks

The office manager converts estimate E-2210 for Midtown Office Park into sales order SO-1187 for $37,900: equipment, labor and crane rental as separate items with class tracking set to the Commercial division. Terms require 50 percent down before the unit is ordered.

Sales OrderClass: Commercial
02

Deposit paid from a Payment Hub link

The office manager sends a click-to-pay link for the $18,950 deposit from the sales order. The property manager pays it on a company card. Payment Hub tokenizes the card and authorizes and captures on the contractor's merchant account.

Click-to-PayTokenized
03

QuickBooks records the deposit

On the next Web Connector run, Payment Hub writes a ReceivePayment for $18,950 to the customer as a prepayment, into Undeposited Funds, referencing SO-1187. The office manager sees it on the customer's balance without entering anything.

Web ConnectorReceivePayment
04

Equipment ordered, job scheduled

With the deposit on the books, the unit is ordered and the crane is scheduled. Nothing about this step involves Payment Hub, which is the point: the office runs the job in QuickBooks as it always has.

Job in Progress
05

Final invoice with the deposit applied

After installation, the office manager creates invoice 14822 from the sales order for the full $37,900. The $18,950 prepayment is applied, leaving $18,950 due. The invoice template carries the payment link, so the customer receives a payment-ready invoice showing the net balance.

Invoice 14822Deposit Applied
06

Customer pays the balance in the portal

The property manager logs into the branded portal, which shows open invoices read from QuickBooks, and pays the $18,950 balance on the saved card. The portal marks the invoice paid immediately.

Customer PortalSaved Method
07

ReceivePayment applied, funds deposited

Payment Hub writes a ReceivePayment applied to invoice 14822 into Undeposited Funds. When the gateway settles, the batch total matches the QuickBooks deposit the office manager records, or Payment Hub records it for her, depending on how the books are configured.

Applied to 14822Undeposited Funds
08

Bank feed matches on the first pass

The bank deposit in the feed matches the QuickBooks deposit to the penny because every payment in it already exists as a transaction. Reconciliation is a review, not a reconstruction, and the job shows fully paid with the deposit and balance correctly separated.

Bank RecReconciled

The detail worth noticing is the deposit. On most contractor setups the deposit sits as an unapplied credit until someone remembers to apply it, or it gets booked to income and corrected at year-end. Here it is a prepayment applied to the final invoice, which is how QuickBooks expects it.

Payment Hub use cases on QuickBooks Enterprise

All 11 Payment Hub use cases run on Enterprise. The ones QuickBooks businesses deploy first are highlighted here, and each links to the full use-case page.

Technical details, for QuickBooks admins and ProAdvisors

The engineering reality of the integration, for the office manager who administers QuickBooks, the IT provider who hosts it, and the ProAdvisor or accountant who keeps the books clean.

QuickBooks Enterprise + Payment Hub FAQ

The questions office managers, bookkeepers, IT providers and ProAdvisors ask before adding Payment Hub to QuickBooks Desktop Enterprise.

Does Clarity Payment Hub integrate with QuickBooks Desktop Enterprise?

Yes. Payment Hub integrates with QuickBooks Enterprise through the QuickBooks Desktop SDK and the QuickBooks Web Connector, Intuit's supported path for third-party applications. Invoice payments, sales order deposits, portal payments and refunds are recorded in QuickBooks as ReceivePayment and Sales Receipt transactions applied to the right invoice.

Customers, invoices, sales orders and the bank register stay in your company file as the single source of truth.

How is this different from QuickBooks Payments?

QuickBooks Payments makes Intuit your processor at Intuit's rates and offers pay-now on emailed invoices, one invoice at a time. Payment Hub connects Enterprise to 19+ gateways on your own merchant account, adds a portal where customers see and pay all their open invoices, handles deposits and progress billing, and sends Level III data on commercial cards. Businesses switch when fees, volume or deposits become a monthly problem.

Which QuickBooks versions does Payment Hub support?

QuickBooks Desktop Enterprise 20 and later, on-premise or hosted. It also works with Premier and Pro on the same SDK path, though most customers we see with the volume to justify it are on Enterprise. QuickBooks Online uses a different integration and a different page.

Do we need to install anything in QuickBooks?

You install and authorize the QuickBooks Web Connector, which is Intuit's own tool and may already be present if you use other integrations. Nothing is added to your company file structure, and no custom fields or templates are required beyond the payment link on your invoice template.

Does it work on Right Networks or other hosted QuickBooks?

Yes. The Web Connector runs on the hosted desktop the same way it does on a local machine. Right Networks and other Intuit-authorized hosts support Web Connector applications, and the connection is outbound only, so nothing needs to be opened on the hosting side.

How does Payment Hub handle deposits on sales orders?

A deposit paid through Payment Hub is recorded as a ReceivePayment prepayment on the customer, referencing the sales order. When the final invoice is created, the prepayment is applied and the customer sees the net balance on the invoice link and in the portal. Progress invoices against an estimate work the same way, one payment per invoice.

We run several company files. Does that work?

Yes. Each company file gets its own Web Connector entry and is mapped to its merchant account and bank account. A customer who deals with two of your entities sees both sets of invoices in one portal login, and each payment lands in the right file.

Can we keep our current merchant account?

Almost always. Payment Hub connects to Worldpay, Adyen, Cybersource, Fortis, PayTrace, Stripe, Braintree, Authorize.Net and more. If your processor is on the list you keep your rates and your relationship. Businesses moving off QuickBooks Payments usually take the opportunity to get competing quotes, and we can help with that.

What happens with Undeposited Funds and bank deposits?

Payments are recorded into Undeposited Funds or directly to a bank account, matching how your books are set up. Payment Hub can also record the Deposit transaction when the gateway settles a batch, so the bank feed matches the QuickBooks deposit without manual grouping. Your bookkeeper chooses which approach at setup.

Does Level III interchange optimization matter for a QuickBooks business?

It matters if your customers pay on commercial or purchasing cards, which is typical for wholesale and manufacturing businesses on Enterprise and less common for contractors billing property owners. When it applies, Payment Hub attaches invoice line detail so those transactions settle at Level III rates, typically 0.5 to 1.0 percent lower.

What is the implementation timeline?

Forty-eight hours from Web Connector access is the standard go-live for the core integration: install and authorize the connector, map accounts, add the payment link to your invoice template, test in a copy of your company file and cut over. Portal branding, gateway migration and recurring setup are added on top without delaying the core.

Who supports the integration, Clarity or our accountant?

Clarity supports the integration and the payment side. Your ProAdvisor, accountant or IT provider keeps supporting QuickBooks as they do today. We work with them during setup so the account mapping matches how they want the books kept.

Related resources

See it live

Invoice and deposit payments, recorded in QuickBooks, on Enterprise.

Book a 30-minute walkthrough and see Payment Hub running against a copy of your own QuickBooks Enterprise company file: Web Connector integration, a deposit on a sales order, ReceivePayment recorded and applied to the final invoice, a branded portal showing live open invoices, Undeposited Funds and deposit handling that matches your bank feed, and Level III enrichment from invoice lines. Live in 48 hours. Your QuickBooks license, templates, lists and other integrations stay intact.

EPICOR KINETIC + PAYMENT HUB · AT A GLANCE Manufacturing verticals supported 10+ Integration method Open REST API Functions / BPM customizations None required Deployment models Cloud + On-prem Typical L3 savings (multi-plant manufacturer) $100K–$200K+/yr MANUFACTURING-FIRST · GATEWAY AGNOSTIC
10+Mfg Verticals
19+Gateways
48hrGo-Live