Should You Receive Payments in Fishbowl, QuickBooks—or Both?

When it comes to handling customer payments, many growing businesses ask the same question:
 Should payments be received in Fishbowl, QuickBooks, or both?
The honest answer is—it depends on how your business operates.
Fishbowl and QuickBooks are designed for different purposes, and understanding where each system shines can help you avoid reconciliation issues, reporting headaches, and workflow confusion. Making the wrong choice doesn’t just create extra work—it can impact accuracy, visibility, and long-term scalability.
Let’s break it down in a practical way.

1. Understanding the Core Difference
At a high level, the difference comes down to what each system is designed to manage:

• Fishbowl records payments against sales orders
• QuickBooks records payments against invoices

2. Best-Practice Payment Split (For Most Businesses)
In most workflows, the cleanest setup looks like this:

• Prepayments and eCommerce payments → Fishbowl
• Invoice payments on terms → QuickBooks

3. Why Invoice Payments Belong in QuickBooks
Handling invoice payments inside QuickBooks offers several practical advantages:

1. Early payment discounts are easier to manage
 QuickBooks is built to track discounts, partial payments, and payment timing without manual workarounds.

2. Invoices rarely match sales orders perfectly
 Scenarios—like multiple shipments, canceled items, or backorders—mean invoices often differ from the original order.

3. Customers may pay multiple invoices with one payment
 QuickBooks is designed to apply a single payment across multiple open invoices seamlessly.

4. Accounts Receivable management lives in QuickBooks
 Fishbowl is not built to manage open A/R. QuickBooks is. This distinction matters when accuracy, compliance, and reporting are priorities—especially for teams relying on professional accounting services.

4. When a Business Requires All Payments in Fishbowl
While not common, some workflows require all payments to be received in Fishbowl—including payments on terms.
One client needed every sales order to show a “Paid” status inside Fishbowl, even when early payment discounts were offered. To support this requirement, two approaches were used:

Option 1:
 Accept full payment in Fishbowl, then add a separate line on the deposit to record the early payment discount and adjust the dollar amount.

Option 2:
 Accept the net payment amount in Fishbowl and add a line to the QuickBooks invoice to record the early payment discount.

It’s important to note that only accepting full payment results in a true “Paid” status in Fishbowl. This workaround works—but it requires discipline, documentation, and clear processes.
This is where thoughtful business process consulting becomes essential.

5. The Risk of an All-or-Nothing Approach
Trying to force one system to handle everything often creates unnecessary complexity. When payments, inventory, and accounting data aren’t aligned properly, businesses experience:

• Reconciliation delays
• Reporting inconsistencies
• Manual adjustments
• Reduced visibility

6. Integration Is the Real Advantage
The real power isn’t choosing Fishbowl or QuickBooks—it’s using them together with clean integration.

When systems are connected properly, api integration services ensure data flows accurately between inventory, sales, and accounting without duplicate entry or guesswork. This improves reliability, reduces manual effort, and supports scalable operations.

Many businesses also rely on quickbooks experts to ensure payment workflows are configured correctly from day one.

Final Thoughts: There’s No One-Size-Fits-All Answer
Whether you should receive payments in Fishbowl, QuickBooks, or both depends on:

• Your payment terms
• Your fulfillment process
• Your reporting needs
• Your growth plans

Book your free consultation here.