1. App Creep, Which Is the Big One
This is the cost that most often exceeds the plan itself, and it accumulates invisibly because every individual decision is defensible.
A reviews app at $15. An email tool at $30. A subscriptions app at $39. An upsell app at $29. A page builder at $24. None of those is unreasonable. Together they are $137 a month — more than the Grow plan, on top of the Grow plan — and most stores are not measuring which of them earns its keep.
What to do: audit quarterly. For each app, write down the number it is supposed to move and check whether it moved. Uninstall anything that fails the test twice. And prefer free apps where a free one does the job — all ten of ours are free to install precisely because conversion tooling should not be the reason a store cannot afford its plan.
2. The Third-Party Gateway Fee
Covered in full in Shopify transaction fees explained, but it belongs on this list because it is the largest avoidable cost most merchants are unaware of.
If you process payments outside Shopify Payments, Shopify charges 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus, on top of your provider's own fee. On Basic at $20,000 a month, that is $400 a month for nothing.
3. Currency Conversion on International Sales
If you sell in currencies other than your payout currency, Shopify Payments applies a conversion fee — typically around 1.5% domestically and about 2% for cross-border sales, varying by region.
This is easy to miss because it does not appear as a line item you approve; it is netted out of the payout. A store doing 40% of its revenue internationally can be paying a meaningful percentage it never budgeted for. If international is a real share of your business, model it explicitly — our international pricing guide covers how to price for it.
4. Shopify Tax
Shopify Tax is free up to a threshold of US sales, then charges 0.35% of orders in US states where you have tax obligations (0.25% on Plus), capped annually.
It only applies to US sales and only above the free threshold, so newer stores never see it. Growing US stores hit it without noticing, because it arrives as a percentage rather than a bill. You can use a third-party tax service instead, which is worth pricing once you are past the threshold.
5. Chargebacks and Refunds
Two distinct costs, both underestimated:
- Chargebacks carry a fee per dispute, and you lose the goods and the original processing fee too. A single $80 chargeback can cost well over $100 all in.
- Refunds do not return the processing fee on the original transaction. Every refund is a small guaranteed loss even when the product comes back saleable.
This makes return rate a payments cost, not just a logistics one. Accurate sizing information, honest photography and realistic delivery estimates are cost control. See why your return rate is high.
6–11. The Rest of the List
| Cost | Typical | What triggers it |
|---|---|---|
| Premium theme | $180–$400 once | Wanting a look the free themes do not offer. Often avoidable. |
| Theme lock-in | Rebuild cost later | Heavy customisation makes switching themes expensive. The real cost of a theme is the second one. |
| Developer work | $50–$150/hour | Anything the theme editor cannot do |
| Shopify POS Pro | $89/mo per location | Selling in person beyond the basic POS |
| Domain and email | $15–$80/year | Shopify sells domains but not mailboxes — you need a separate provider |
| Paid acquisition | Unbounded | The largest cost of all for most stores, and the one least often modelled before launch |
On that last row: the cost of Shopify is almost never what makes or breaks a store. Customer acquisition cost is. A store spending $40 a month on Shopify and $4,000 on ads that do not convert has a conversion problem, not a platform problem. Our acquisition cost benchmarks are the better place to spend your attention.
A Budget That Survives Contact With Reality
Build the number this way instead of from the pricing page:
- Plan: $39 (Basic, monthly)
- Domain: $1.25
- Apps, realistically: $0–$60 — be honest about which you will actually install
- Payment processing: 2.9% + 30¢ per order, plus conversion if you sell internationally
- A contingency for refunds and chargebacks: 1–2% of revenue
For a store doing $5,000 a month, that lands around $260–$320 all in, against the $39 the pricing page implies. That is not Shopify being dishonest — it is what running a store costs. Budget for the real number and nothing on this page will surprise you.
Frequently Asked Questions
What is the biggest hidden cost of running a Shopify store?
Apps. Five modestly priced apps at $15 to $39 each comes to around $137 per month, which exceeds the Grow plan and sits on top of it. Unlike the plan, app spending accumulates one defensible decision at a time and is rarely audited against what each app actually earns.
Does Shopify charge for currency conversion?
Yes. When you sell in a currency other than your payout currency, Shopify Payments applies a conversion fee, typically around 1.5% domestically and about 2% cross-border, varying by region. It is netted out of your payout rather than billed, which is why it is easy to miss.
What is Shopify Tax and does it cost extra?
Shopify Tax calculates US sales tax. It is free up to a threshold of US sales, after which it charges 0.35% of orders in states where you have obligations (0.25% on Plus), with an annual cap. It applies only to US sales, so newer and non-US stores never encounter it.
Do I get my processing fee back when I refund an order?
Generally no. The card processing fee on the original transaction is not returned when you issue a refund, so every refund is a small guaranteed loss even if the item comes back in saleable condition. This makes return rate a direct payments cost.
How much should I actually budget for a new Shopify store?
About $40 per month covers the plan and domain with free themes and free apps. Once you add realistic app spend, payment processing and a contingency for refunds, a store doing $5,000 per month typically runs $260 to $320 all in. Paid advertising, if you use it, will usually exceed all of the above combined.
Is a paid Shopify theme worth it?
Usually not at the start. Shopify's free themes are fast, responsive and maintained by Shopify. The larger cost is not the $180 to $400 purchase but the lock-in: once a theme is heavily customised, moving to a different one means redoing that work. The real cost of a theme is the second theme.
💡 Ready to put this into practice? Shopify's free 3-day trial — then $1/month for 3 months, plus 1% of sales back in credits — is long enough to set it up and see the numbers. Start your free trial → (affiliate link)