Shopify QuickBooks Integration Pricing and Shopify to QuickBooks Sync App Costs Compared
October 2026 · Reconciler
Try it while you read
This is the tie-out board Reconciler gives you: both sides side by side, matches explained in plain English, exceptions flagged. Read-only, and it never moves money.
Read-only ยท Never moves money
A Shopify QuickBooks integration costs between $0 and about $300 a month for most US stores. Checked on October 6, 2026, Intuit's own Shopify Connector by QuickBooks installs from inside QuickBooks Online with no separate fee listed. Paid sync apps on the Shopify App Store start at $5 to $30 a month for basic order sync, $29 to $49 for A2X and MyWorks at a few hundred orders, and $65 to $79 for Synder and Webgility. Nearly every paid option prices on monthly order volume, so the honest answer depends on how many orders you ship.
Price is only half of the buying decision. Every tool below moves Shopify activity into QuickBooks. None of them proves that what QuickBooks now shows agrees with the Shopify payouts that actually reached your bank, and that gap is where most Shopify bookkeeping goes wrong. We read each vendor's own App Store listing or pricing page on October 6, 2026, and the tables show only what they publish.
How much does a Shopify QuickBooks integration cost?
Expect $0 for Intuit's connector, $5 to $60 a month for a basic order sync up to a few thousand orders, $29 to $115 for A2X or $49 to $109 for MyWorks depending on volume, and $65 to $350 a month for Synder or Webgility, which add other channels. Bookkeep is the outlier: it prices on annual revenue rather than order count.
| Option | Published price, checked October 6, 2026 | What the price counts | Trial |
|---|---|---|---|
| Shopify Connector by QuickBooks (Intuit) | No separate fee listed; installs from Integrations in QuickBooks Online | No cap published; imports up to one year of history | Not applicable |
| MyWorks Sync | Launch $0 for 20 orders, Rise $24 for 100, Grow $49 for 300, Scale $89 for 1,000, Soar $109 unlimited; $19, $39, $69 and $99 billed yearly | Orders a month | 14 days |
| A2X | Mini $29 for 200 orders, Basic $45 for 500, Professional $79 for 2,000, Advanced $115 for 5,000 | Orders a month, COGS from Basic up | 30 days |
| Link My Books | Lite plans on its App Store listing: $21 for 200 orders, $41 for 1,000, $60 for 5,000, $100 for 10,000 | Orders a month | Not stated on the listing |
| Synder | Basic $65, Essential $129, Pro $299, Pro Max $599 a month; $624, $1,236, $2,880 and $5,760 billed yearly | Sales transactions: 500, 3,000, 20,000 and 40,000 on its App Store listing | 15 days |
| Webgility | Pro $79 ($69 billed yearly) for 300 orders, Advanced $149 ($129) for 800, Complete $349 ($299) for 1,500; extra orders $10 a month per 500 | Orders across sales channels | Free trial offered |
| SyncTools | Lite $19 for 200 orders, Basic $39 for 500, Standard $59 for 2,000, Plus $89 for 5,000; about 12% off yearly | Orders a month | 30 days |
| QuickBooks Bridge by Parex | Silver $15 for 100 orders, Gold $30 for 500, Platinum $45 for 1,500, Platinum Plus $100 for 10,000, plus 2 to 10 cents per extra order | Orders a month | 7 days |
| Bold QuickBooks Sync Pro | Starter $19.99 for 200 orders, Growth $39.99 for 500, Enterprise $59.99 unlimited; overage capped at $99.99 | Orders a month | 14 days |
| QuickSync | Starter $5 for 100 orders, Plus $10 for 500, Pro $20 for 1,000, Premium $30 unlimited | Orders a month, plus 2 to 5 cents per extra order | 14 days |
| Bookkeep | Lite $19 to $200,000 revenue, Starter $49 to $500,000, Growth $99 to $1.5 million, Pro $199 to $5 million a year | Annual revenue through connected channels | 14 days |
Two caveats on the listings. Synder's own website has quoted lower transaction limits for the same plan names than its Shopify listing shows, so confirm the limit in writing at your volume. Link My Books labels its App Store plans Lite, and its own site sells fuller plans at different prices, so check which features the Lite tier leaves out before you compare it with A2X.
Is the Shopify QuickBooks integration free?
Intuit's connector costs nothing beyond your QuickBooks Online subscription. Its help article lists every QuickBooks Online plan from Simple Start to Advanced as compatible. It imports sales, refunds, fees and payouts, records each order as a sales receipt with its fees as an expense, and groups them into deposits that represent each Shopify payout. You pick a start date up to one year back. It does not connect to QuickBooks Desktop.
For a single US store with modest volume, the free connector is the right place to start. Stores move to a paid app for three reasons. They ship enough orders that one QuickBooks record per sale buries the ledger, and they want one summarized entry per payout instead. They need cost of goods sold posted automatically. Or they sell on Amazon, Etsy, PayPal or Stripe as well and want every channel mapped the same way in one tool.
What does each Shopify to QuickBooks app cost at 200, 1,000 and 5,000 orders?
This is what each published ladder charges one Shopify store at three monthly volumes, monthly billing, with the yearly rate in brackets where the vendor publishes one. Where a plan charges per extra order, we priced the cheaper of paying the overage or moving up a plan. Webgility's $10 blocks of 500 extra orders are added to the cheapest plan that fits.
| App | 200 orders a month | 1,000 orders a month | 5,000 orders a month |
|---|---|---|---|
| Shopify Connector by QuickBooks | $0 | $0 | $0 |
| QuickSync | $10 | $20 | $30 |
| Bold QuickBooks Sync Pro | $19.99 | $59.99 | $59.99 |
| SyncTools | $19 | $59 | $89 |
| Link My Books (Lite) | $21 | $41 | $60 |
| QuickBooks Bridge by Parex | $25 | $45 | $100 |
| A2X | $29 | $79 | $115 |
| MyWorks | $49 ($39) | $89 ($69) | $109 ($99) |
| Synder | $65 ($52) | $129 ($103) | $299 ($240) |
| Webgility | $79 ($69) | $159 ($139) | $239 ($219) |
| Bookkeep | Not order based. At a $60 average order, 200, 1,000 and 5,000 orders a month are about $144,000, $720,000 and $3.6 million a year, which lands on Lite $19, Growth $99 and Pro $199 | ||
The cheapest paid tools are order-sync utilities that post each sale; they are fine at low volume and get noisy fast. The accounting-grade tools, A2X, Link My Books and MyWorks, cost $29 to $115 at these volumes and post summarized settlements or let you choose summaries. Synder and Webgility cost more because they also cover Amazon, PayPal, Stripe and other channels from one account, which matters only if you sell there.
Which Shopify QuickBooks integration is best for my store?
If Shopify is your only channel and you ship a few hundred orders a month, start with Intuit's connector and pay only when it stops fitting. If you want one clean entry per payout with fees, refunds and COGS split out, A2X and Link My Books are built for that, and MyWorks is the pick when you also need inventory and products synced both ways. If Shopify is one of several channels, Synder or Webgility keep them in one mapping, and Bookkeep is worth pricing when revenue is high but order values are small. Our A2X vs Link My Books pricing comparison works through those two ladders order by order.
Watch the margin side too. A sync app tells QuickBooks what sold and what Shopify kept in fees; it does not tell you what each order cost you to win. If paid ads drive most of your Shopify sales, put the ad spend next to the payouts with a marketing dashboard that ties ad channels to store revenue before you decide a channel is profitable.
Why do Shopify payouts still not match QuickBooks after the sync?
Because a sync app copies Shopify's records, and Shopify's records are not your bank deposits. One payout bundles several days of orders, minus processing fees, minus refunds and chargebacks that can belong to sales from weeks earlier. Orders paid through PayPal, Shop Pay Installments or a manual gateway settle on their own schedule and never appear in the Shopify payout at all. Gift cards are sold in one period and redeemed in another. Any of these can leave a deposit in QuickBooks that does not equal the line on your bank statement, and if the bank feed also creates that deposit, it lands twice.
The result is the familiar month-end problem: Shopify, the bank and QuickBooks each show a different total, and nobody can say which orders explain the difference. That walk from orders to payouts to deposits is Shopify payout reconciliation, and none of the sync apps above sells it as the job they do.
Do I need a sync app and reconciliation software?
Most Shopify sellers on QuickBooks need one tool to move the data and one way to prove it is right. The sync moves data. Ecommerce payment reconciliation software checks the result against the money that arrived. Reconciler connects QuickBooks Online read-only, takes your bank statement as a CSV upload (Mercury and Brex connect directly) and your Shopify payout export as a CSV, and matches each payout to the bank deposit and to the deposit your sync posted in QuickBooks, line by line, with a plain English reason under every pair and every exception flagged. It does not split a payout into orders; that stays the sync app's job. It never posts to QuickBooks and never moves money, so it runs next to whichever sync you choose. With QuickBooks connected it is $89 a month billed yearly, or $179 month to month.
If you also take payments through Stripe, PayPal or Square, the same choice comes up with different ladders. See Stripe QuickBooks integration pricing, PayPal QuickBooks integration pricing and Square QuickBooks integration pricing, plus Amazon QuickBooks integration pricing if you also sell on Amazon, and the QuickBooks reconciliation page for how the ledger connection works.
What should I ask a vendor before paying for a Shopify sync?
- What counts as an order? Ask whether refunds, edited orders, draft orders and point-of-sale sales count toward the limit, because each can push you into the next plan.
- Does it post each order or one entry per payout? A payout summary keeps QuickBooks readable at volume; per-order detail helps when a customer disputes one charge.
- How does it treat PayPal and other gateways? Orders paid outside Shopify Payments settle separately. Ask where those land in QuickBooks.
- Does it post cost of goods sold? A2X includes COGS from Basic, MyWorks syncs cost and inventory, and the basic order syncs mostly do not.
- How far back can it import? Intuit's connector goes back up to one year; others vary by plan.
- How will I know the Shopify clearing account is right at month end? If the answer is "check it by hand", plan for that job or for a tool that does it.
Prices in this category change often, so confirm any figure here on the vendor's own page before you buy. If the sync already runs and the real problem is proving that Shopify, the bank and QuickBooks agree, you can see Reconciler's plans and match your own Shopify payouts the same day.
See your accounts tie out to $0.00
Upload your bank and ledger exports or connect supported accounts read-only. Reconciler matches transactions, flags what does not add up, and explains every match, so your books close faster. Read-only, never moves money.