Payment Gateway Integration: Connecting Stripe, Square, and PayPal to Your Business

Taking payments is one thing. Getting that payment data into the rest of your business systems — accounting, CRM, inventory, reporting — is something else entirely.

Most businesses start with a payment gateway that handles transactions well enough: Stripe for online payments, Square for in-person, PayPal for the customers who insist on it. The gateway processes the money. But then someone has to reconcile those payments against invoices, update customer records, track subscription revenue, handle refunds, and make sure the accounting is right.

If that “someone” is a person with a spreadsheet, you have an integration problem.

What Needs to Connect

Payment gateways generate a wealth of data with every transaction — far more than just “payment received.” The question is where that data needs to go.

Accounting Software

This is the critical connection. Every payment needs to appear in your accounting system (Xero, MYOB, QuickBooks) as a matched transaction. But it’s not as simple as syncing the gross amount.

What your accounting system needs:

• Gross payment amount — what the customer paid
• Gateway fees — Stripe takes 1.75% + 30c per transaction in Australia; Square takes 1.6% for tap/insert. These are expenses that need recording.
• Net settlement amount — what actually hits your bank account
• GST on fees — payment processing fees include GST (in Australia), which you can claim as input tax credits on your BAS
• Invoice matching — linking the payment to the correct invoice so it’s marked as paid, not sitting as an unmatched bank deposit

CRM

When a payment comes through, your CRM record should reflect it. This seems obvious, but plenty of businesses have sales teams who can’t tell whether a customer has actually paid without logging into the payment gateway separately.

Useful CRM updates from payment events:

• Deal/opportunity marked as won when payment is received
• Customer record updated with payment method on file
• Subscription status visible on the contact record
• Failed payment alerts triggering follow-up tasks
• Lifetime payment value calculated automatically

Operations and Fulfilment

For businesses that deliver goods or services after payment, the payment event triggers the next step. An e-commerce order needs fulfilment. A service booking needs scheduling. A software subscription needs provisioning. If these systems aren’t connected to your payment gateway, someone is manually checking for payments and kicking off the next step.

Stripe, Square, and PayPal: Integration Differences

Not all payment gateways are created equal when it comes to integration.

Stripe

Stripe is the developer’s favourite — and for good reason. Its API is exceptionally well-documented, its webhook system is robust, and it supports complex payment flows (subscriptions, metered billing, marketplace payments, payment links).

Integration strengths: Real-time webhooks for every event type. Detailed metadata on every transaction. Excellent subscription management. Strong support for custom payment flows.

Watch out for: Stripe’s flexibility means there are many ways to implement the same thing. If your Stripe setup wasn’t built with integration in mind, the data structure might not map cleanly to your accounting or CRM. Stripe also batches payouts, so bank reconciliation requires understanding their settlement schedule.

Square

Square excels at in-person payments and is increasingly capable for online transactions. Its ecosystem includes POS, inventory, appointments, and team management — which means some integrations are handled natively within Square’s own tools.

Integration strengths: Good native integrations with Xero and QuickBooks. Built-in POS and inventory. Simple webhook system.

Watch out for: Square’s API is less flexible than Stripe’s for custom payment flows. If you need complex billing logic — metered usage, tiered pricing, custom invoicing — Square has limitations. Its reporting API also has gaps compared to Stripe.

PayPal

PayPal remains essential for many businesses — customers trust it, and in some markets it’s expected. But integrating PayPal with business systems is historically more painful than Stripe or Square.

Integration strengths: Broad consumer adoption. Good buyer protection. Supports invoicing, subscriptions, and marketplace payments.

Watch out for: PayPal’s API has gone through multiple generations (Classic, REST, current GraphQL-based Checkout). Legacy integrations are common and poorly documented. Webhook reliability has historically been inconsistent. Fee structures are complex and vary by transaction type, making accurate accounting harder.

Payment Reconciliation: The Hard Part

Reconciliation is where payment integration gets genuinely difficult. Here’s why.

Batch settlements. Stripe and Square don’t send individual payments to your bank. They batch transactions into periodic payouts — daily or weekly. Your bank sees one deposit of $4,237.50. Your Stripe dashboard shows 47 individual transactions minus fees. Your accounting system has 47 invoices that need matching. Without proper integration, someone is manually ticking off each one.

Fees within fees. A $100 payment through Stripe incurs a $2.05 fee (1.75% + 30c). That fee includes GST ($0.19). Your accounting entry needs to record $100 revenue, $2.05 processing expense, and $0.19 GST credit. Multiply this by hundreds of transactions per month, and manual tracking is not viable.

Refunds and chargebacks. A refund isn’t just the reverse of a payment. The original invoice needs crediting, the COGS may need reversing (if a product was returned), the gateway fee is partially (Stripe) or fully (PayPal) non-refundable, and the settlement payout is reduced. Each refund touches accounting, inventory, and CRM.

Currency conversion. If you accept payments in multiple currencies, the exchange rate at the time of payment differs from the rate at settlement. Your accounting system needs both rates to handle foreign exchange gains/losses correctly.

Subscription Management

Subscription billing adds another layer of complexity. Stripe and PayPal both support recurring payments, but the business system integration goes beyond just collecting money.

What needs to happen when a subscription event occurs:

• New subscription: CRM record updated, service provisioned, welcome workflow triggered
• Renewal payment: Invoice created in accounting, payment matched, customer record updated
• Failed payment: Retry logic triggered in the gateway, CRM flagged, follow-up task created for the team
• Cancellation: Service deprovisioned, CRM updated, retention workflow triggered (if you have one)
• Upgrade/downgrade: Proration calculated, new invoice generated, CRM record updated with new plan

Most businesses handle the initial subscription setup well but let the ongoing lifecycle events fall through the cracks. Failed payments go unnoticed for weeks. Cancellations don’t update the CRM. Upgrades aren’t reflected in reporting.

Choosing Your Integration Approach

For simple setups (one gateway, standard pricing, under 200 transactions per month): dedicated reconciliation tools like Amaka or A2X connecting your gateway to Xero or QuickBooks will handle accounting sync well. CRM integration via Zapier or Make can push payment events to your sales tools.

For moderate complexity (multiple gateways, subscriptions, 200-1,000 transactions per month): you’ll likely need a combination of reconciliation tools for accounting plus middleware for CRM and operations. Expect to spend time configuring and maintaining these.

For complex setups (custom billing logic, high volume, multi-currency, subscription lifecycle management): a purpose-built integration is usually the most reliable and cost-effective option. The upfront investment pays off through accurate data, eliminated manual reconciliation, and payment events that trigger the right downstream actions automatically.

The goal isn’t to connect your payment gateway for the sake of it. It’s to create a flow where money in equals accurate records everywhere — accounting that reconciles automatically, CRM records that reflect reality, and operations that kick off the moment payment clears. When that works, your finance team stops chasing transactions and starts providing the insights your business needs to grow.