Shopify makes the payment-processor choice feel obvious: just turn on Shopify Payments and you're done. For most new stores, that's actually the right call — but it isn't always.
Picking from the best ecommerce payment processors for new Shopify stores comes down to four things: your monthly volume, your average order value, the products you sell, and whether Shopify Payments is even available in your country. Below is the practical decision tree we walk new merchants through.
Why Shopify Payments is the default — and what you give up
Shopify Payments (powered by Stripe under the hood) waives Shopify's third-party transaction fee, which is the headline reason to use it. On the Basic plan, that's 2% per order you'd otherwise pay on top of your processor's rate. On Shopify Plus, it's 0.15%.
On a $50,000/month store on the Basic plan, the third-party fee alone is $1,000/month. That's why most new Shopify stores default to Shopify Payments — the math is hard to argue with at small scale.
What you give up: limited high-risk product acceptance, no negotiating on rates until you're well past $1M/year, and account hold risk if Shopify's risk team flags your store. For a brand-new clothing or accessories shop, none of that matters. For a supplements, vape, or CBD store, all of it does.
Stripe — the runner-up most stores never need to switch to
Stripe is what powers Shopify Payments, so the underlying rates are nearly identical. The reason to use Stripe directly on Shopify (and pay the 2% Shopify third-party fee) is when you need:
- Stripe Connect for marketplace splits or affiliate payouts.
- Stripe Billing for complex subscription dunning that Shopify's native subs can't handle.
- Stripe Radar custom rules that Shopify Payments doesn't expose.
- Stripe Treasury / Issuing if you're embedding financial services.
PayPal — almost always a complement, not a replacement
Adding PayPal as a secondary option on a Shopify store typically lifts conversion by 3–8%, especially for buyers over 35 and international shoppers. PayPal as your *primary* processor on Shopify is a mistake — the rates aren't competitive and the dispute process is painful.
The right move: keep Shopify Payments primary, add PayPal Express Checkout for the share of customers who only trust paying through PayPal. Same applies to Apple Pay and Shop Pay — they're conversion tools, not processors to compare on rate.
When a new Shopify store should look outside Shopify Payments
Shopify Payments isn't the answer for every new store. Skip it (or plan to switch later) if any of these apply:
- You sell on Shopify's restricted/prohibited list — supplements that make health claims, CBD/hemp, vape, firearms, adult, ticketing for high-chargeback events.
- You're in a country Shopify Payments doesn't support — most of LATAM, much of APAC, parts of Eastern Europe.
- Your AOV is over $500 and most customers are B2B — you'll save more on a dedicated processor with Level 2/3 data support.
- You're doing pre-orders longer than 30 days — Shopify's reserve policies can be brutal here.
Real fee math on $20k, $50k, and $250k/month
Here's how the best ecommerce payment processors for new Shopify stores actually compare at three common volume tiers, assuming Shopify Basic ($39/mo) and a typical 2.4% effective ecommerce mix:
- $20k/month — Shopify Payments: ~$580/mo all-in. Stripe direct: ~$580 + $400 third-party fee = $980. Winner: Shopify Payments by a wide margin.
- $50k/month — Shopify Payments: ~$1,450/mo. Dedicated interchange-plus: ~$1,200 + nothing (Shopify charges the 2% only on third-party gateways using their checkout, not when you bypass it). Winner: still Shopify Payments for simplicity.
- $250k/month — Shopify Payments: ~$7,250/mo. Interchange-plus on Shopify Plus (0.15% third-party): ~$5,800 + $375 = $6,175. Winner: dedicated processor saves ~$13k/year.
Our shortlist for new Shopify stores
If you're launching a new Shopify store today, here's our practical ranking:
- Default: Shopify Payments + PayPal Express + Shop Pay — covers 90%+ of buyers with one click.
- High-risk vertical: NMI or Authorize.Net via a high-risk acquirer — keeps Shopify checkout, swaps the gateway.
- Subscription-heavy: Stripe + Shopify subscription app — better dunning and card-updater behavior.
- B2B / high-AOV: dedicated processor with Level 2/3 support — the savings start mattering above $50/mo in commercial card volume.
For 80% of new Shopify stores, the answer to best ecommerce payment processors for new Shopify stores is: turn on Shopify Payments, add PayPal Express, and revisit at $100k/month. The other 20% — high-risk verticals, B2B-heavy, or subscription-heavy — should benchmark a dedicated processor before launch, not after a chargeback storm forces the issue.
Frequently asked questions
Is Shopify Payments the cheapest option for a new Shopify store?+
For most new stores under $50k/month, yes — because it waives Shopify's 2% third-party transaction fee. Above $100k/month, a dedicated interchange-plus processor on Shopify Plus typically beats it.
Can I use Stripe and Shopify Payments together?+
Not as parallel processors. Shopify Payments IS Stripe under the hood, so there's no benefit. You can run Stripe alongside Shopify Payments only via apps for specific flows (subscriptions, marketplaces).
Will I get approved for Shopify Payments if I sell supplements?+
Generic vitamins yes, anything making health claims or in the gray-area categories (kratom, CBD, weight loss) almost always no. Plan for a high-risk processor and use Shopify only as the storefront.
Does adding PayPal hurt my Shopify Payments rates?+
No. Shopify Payments rates are based on plan tier, not on whether you also offer PayPal. Adding PayPal almost always nets positive on conversion.
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