The Hidden Challenge Facing Shopify Agencies & Accountants
TL;DR:
- Agencies waste ~80 hrs and ~$900/mo on DIY integrations
- Complex client needs break generic connectors for Shopify QuickBooks
- The solution is a highly customizable real-time, two-way sync that’s Built for Shopify
“Accounting is too important to mess up. If it’s wrong once, it keeps carrying over like a math mistake.” —Katherine, founder at Maze, a Canada-based Shopify Select Partner agency.
Shopify agencies aren’t just building storefronts anymore—they’re building operational backbones. And when those backbones depend on accounting data, reliability matters—which is why many agencies now choose integrations Built for Shopify rather than patchwork connectors.
“Accounting has been something top of mind since day one,” explains Katherine, “It is a core challenge for every business.”
Connecting Shopify to QuickBooks looks simple. Then refunds, split payments and B2B terms show up, and the whole thing buckles, preventing agencies from focusing on their core strengths: design, conversion optimization, and scaling stores.
Why Ecommerce Accounting Integration Matters for Agencies
For Shopify agencies serving merchants in the $1M-$10M GMV range, accounting integration isn’t just a nice-to-have—it’s essential for client success. These businesses face increasingly complex challenges:
- Mixed B2B and B2C requirements with different accounting workflows
- Order modifications creating sync nightmares (forgotten discount codes, size changes, refunds)
- Lack of visibility into the integration process
- Constant “babysitting” of accounting systems
As Katherine from Maze puts it bluntly: “Accounting is too important to mess up. If it’s wrong once, it keeps carrying over like a math mistake.”
Common Pitfalls For Agencies To Avoid
1. Underestimating Integration Complexity
Many agencies underestimate the technical complexity of accounting integration, treating it as a simple data transfer problem rather than a sophisticated financial workflow challenge.
For example, Maze initially tried DIY integration approaches that proved extremely time-consuming and ineffective. If you need multiple apps, custom APIs, and daily monitoring, it’s not a solution—it’s a liability.
2. Choosing Tech Based on Price Alone
The least expensive solution often becomes the most costly in terms of time, errors, and lost opportunities. That free connector app turns into $10,000 in reconciliation costs and client frustration.
3. Neglecting Wholesale Requirements & Edge Cases
B2B functionality creates unique accounting challenges that many integration solutions can’t handle.
“The trouble starts after checkout, when Shopify and QuickBooks operate in silos,” explains Katherine. “Invoices are rebuilt by hand, customers lack real-time visibility into balances, and inventory lags between systems.”
Additionally, details like refunds, partial payments, and gift card support are where most integrations fail.
4. Failing to Consider Tax Compliance
The sales tax landscape for ecommerce is increasingly complex, with economic nexus laws creating obligations across multiple jurisdictions. Ecommerce tax has become a moving target for Shopify sellers, making proper accounting integration essential for compliance.
5. Building Without Client Growth in Mind
What works for a client today may fail them tomorrow as their business scales. Agencies should select solutions that accommodate growth. Your client might need their orders synced as sales receipts today, but as the business scales, a combination of daily summaries and invoices for wholesale orders might make more sense.
Best Practices for Agencies Syncing Ecommerce and Accounting
From Maze’s hard-earned experience and industry benchmarks, these best practices consistently make syncing smoother for agencies and their clients:
1. Start With Clean Foundations
Don’t bolt automation onto messy data. Get the basics right: every order, refund, fee, and tax detail must flow consistently from Shopify into QuickBooks or Xero
✅ Pro tip: Use integrations carrying the “Built for Shopify” badge—these are vetted for stability, data accuracy, and long-term support.
2. Differentiate B2C and B2B Workflows
B2C clients usually need sales receipts or daily summaries, while B2B transactions require estimates or invoices with terms like Net 30 or Net 60. A good sync must accommodate both—otherwise agencies juggle separate workflows that introduce errors.
Here’s what a good hybrid workflow looks like:
Using the free Shopify Flow app, Wholesale and Retails orders are tagged accordingly.
The QuickBooks sync app automatically recognizes the different tags and syncs them in different ways, for example:
- Order tagged “Wholesale” → QuickBooks Integration syncs it as an open Invoice + Net 30 → Invoice gets paid → QuickBooks Integration auto-marks Shopify order as Paid
- Order tagged “Retail” → QB Integrations syncs it as a Sales Receipt or a Daily summary together with other Retail orders → Shopify Payout arrives → QB Integration automatically matches the payout to retail sales → Reconcile in one click (‘Match’ in QB)
3. Avoid Over-Integrating
Connecting every sales channel directly to accounting is chaos. The smarter move is to centralize through the main ecommerce store (on Shopify or WooCommerce), then sync into accounting with one reliable integration.
4. Prioritize Real-Time Syncing
For scaling businesses, manual reconciliation and DIY setups typically cost $1.8k–$2k per month in labor and software fees; accounting automation reduces that cost tenfold and eliminates manual tasks.
5. Choose Tools That Scale With Growth
Spreadsheets collapse the minute volume spikes. Tools should support individual orders, daily summaries, or hybrid setups—so agencies can tailor syncing to each client’s growth stage.
The Methods Agencies Try First (and Why They Fail)
Agencies often test multiple approaches before finding the right sync strategy. Maze’s journey is a cautionary tale for peers:
1. Manual entry
Works for 5 orders a day. Fails spectacularly at 50. The hours pile up, errors compound, and suddenly accountants spend more time reconciling spreadsheets than analyzing performance.
2. Generic (free) connector apps
Many agencies default to low-cost, one-way sync tools. These handle simple sales receipts but fall apart with refunds, split payments, or B2B workflows. Katherine described the fallout:
“With a lot of other integrations, you have to go in quite regularly and check up on it. Oh, I have fifty orders that haven’t been processed because you’re missing a sync with taxes.”
3. Custom-built automations (Zapier, Make, etc.)
DIY looks cheap until you’re two months in and paying ~$1,000 a month just to keep the duct tape from peeling.
“It was a real headache,” Katherine recalled. “We had to chat with Make, chat with QuickBooks… it took us two months just to get anything to process.”
Why Agencies Choose MyWorks (After Trying Everything Else)
After burning time and money on alternatives, Maze standardized on MyWorks as their integration of choice. Here’s why:
Built Specifically for Shopify and WooCommerce
“As an agency, our clients trust us as their advisers. We have the responsibility to make good choices on their behalf. We don’t add a lot of new apps to our tech stack unless that app has been really vetted.”
MyWorks is the only accounting integration carrying the Built for Shopify badge, giving agencies confidence in recommending the sync. The app is conveniently managed right from the backend of the ecommerce platform.
The Built for Shopify status is not the only MyWorks achievement that gives agencies and accountants confidence in recommending the tool to their clients. MyWorks is also the official QuickBooks sync for WooCommerce and a Platinum-level Intuit (QuickBooks) partner.
Real-Time, Two-Way Sync
MyWorks maintains constant data flow between Shopify and QuickBooks, eliminating the manual tasks and monitoring required with other solutions.
“With MyWorks, accounting goes from being a constant babysitting job to something you barely think about—because it just works,” explains Katherine.
Support for Complex Workflows
The platform handles B2B and B2C orders differently, supporting sales receipts, daily summaries, estimates, invoices with payment terms, and even mixed workflows by syncing based on order tag.
Quick Implementation
Katherine set up her first client’s MyWorks integration in under 60 minutes, compared to over 80 hours spent on custom solutions.
“With Make, we invested about ten hours a week for about eight weeks. That’s eighty hours to set up. And at that point, it was set up, but it wasn’t working. With MyWorks, it took us an hour. You’re saving us seventy-nine hours from setup alone.”
The Competitive Advantage of Accounting Automation
Agencies that want to future-proof client relationships need to see ecommerce accounting not as an afterthought, but as core infrastructure. For those that have mastered their tech stack, the added efficiency becomes their competitive edge.
By implementing the best practices outlined here and avoiding common pitfalls, agencies can deliver operational efficiency through integrated accounting. That frees both themselves and their clients to focus on what matters most: building and scaling successful ecommerce businesses.
As Katherine from Maze summarizes: “When I don’t have to think about MyWorks, that’s when I know it’s working. Syncing just happens in the background, and our clients can focus on selling.”
Ready to Make Accounting Efficiency Your Competitive Edge?
MyWorks offers the only Shopify accounting integration that carries the prestigious Built for Shopify badge, delivering real-time, two-way sync between Shopify and QuickBooks. See how it can help your agency deliver better results with less effort.
Book a demo to see MyWorks in action →
FAQs: Syncing Shopify and Accounting for Agencies
What’s the best way for agencies to sync Shopify with accounting software?
The most reliable approach is to centralize all ecommerce activity through Shopify and use a purpose-built integration like MyWorks Sync to connect it to QuickBooks or Xero. This setup eliminates manual data entry, ensures two-way syncing of orders, refunds, and inventory, and supports both B2C (sales receipts or daily summaries) and B2B (invoices or estimates) workflows.
Why do most agencies struggle with ecommerce accounting integration?
Because they start with the wrong tools. Many rely on one-way connectors or DIY automations that break under real-world complexity—refunds, split payments, and tax variations. As Maze’s co-founder Katherine put it, “With a lot of other integrations, you have to go in regularly and check up on it. I have a full-time job already; I don’t want to babysit accounting.”
Can you use Make or Zapier to sync Shopify and QuickBooks?
You can—but you’ll regret it. Custom Make/Zapier builds are expensive, slow, and fragile. Shopify Select Partner agency Maze spent two months building one that cost roughly $1,000/month in fees and constant maintenance. A native sync like MyWorks does the same job in under an hour for a fraction of the cost.
How can agencies manage B2B and B2C accounting in the same Shopify store?
Use integration software that distinguishes between order types. MyWorks, for instance, can automatically sync B2C transactions as sales receipts (for prepaid customers) and B2B transactions as invoices with Net 30 or Net 60 terms, based on Shopify order tags. This keeps reporting and reconciliation clean without the need for multiple stores.
What are the most common pitfalls when syncing ecommerce and accounting?
- Treating sync setup as an afterthought rather than a foundation.
- Using multiple disconnected apps for payments, taxes, and orders.
- Failing to test edge cases like refunds or multi-payment orders.
- Ignoring how your client’s accounting team works.
Avoiding these errors saves agencies dozens of hours in reconciliation each month.
How long does it take to set up a proper Shopify–QuickBooks sync?
With tools like MyWorks, setup takes under 60 minutes. In contrast, manual or DIY methods can stretch to 80+ hours, especially if you’re handling multiple sales channels or wholesale clients.
Why do agencies choose MyWorks over other integrations?
Because it’s the only ecommerce accounting integration Built for Shopify, offering real-time two-way syncing, flexible order mapping, and advanced financial controls like class, location, and tag-based automation. It scales with your clients’ stores—without breaking when volume spikes.
What kind of results can agencies expect from using MyWorks?
Agencies like Maze report:
- 79+ hours saved per client setup compared to DIY tools.
- 20% efficiency gains in ongoing accounting processes.
- Up to $900/month saved compared to Make or Zapier workflows.
- Fewer sync errors, cleaner books, and happier clients.
How do I sync QuickBooks with all sales channels (Amazon, Etsy, Faire, etc.)?
MyWorks lets you sync all your sales channels to QuickBooks by using Shopify as your central hub. Connect your sales channels to Shopify, not directly to QuickBooks. Then use MyWorks to feed a single standardized stream into accounting. Fewer connections, fewer fires.
