These are the five reasons that show up repeatedly when merchants research switching.
Shopify Payments charges 2.4%–2.9% on every transaction, regardless of card type. A regulated debit card costs 0.05% + $0.21 at interchange. You pay the same 2.9% as a premium rewards card. There is no interchange-plus option at any Shopify plan level.
Shopify charges 0.5%–2.0% extra on every transaction processed by a non-Shopify processor. This surcharge makes switching processors more expensive on Basic and mid-tier plans. It's a financial wall designed to keep you from leaving.
Payment issues route through the same support queue as storefront questions. There is no dedicated account manager, no direct phone line for payment disputes, and no specialist who knows your processing history.
You don't have your own merchant ID. Shopify Payments pools your transactions under a shared master account. Account holds, elevated chargeback ratios, or policy changes at Shopify can affect your funds even if you've done nothing wrong.
Shopify Payments can't process phone orders, invoices, in-person retail outside of Shopify POS, or transactions on a non-Shopify checkout. A dedicated merchant account processes everywhere you sell.
Shopify Payments offers no mechanism to pass processing fees to customers. Cash discount and surcharge programs — which can eliminate processing costs entirely — are not available through Shopify Payments at any tier.
Quick Answer
The best Shopify Payments alternative for merchants processing $20K+/month is a dedicated merchant account with interchange-plus pricing. Shopify charges 0.5%–2.0% extra on any third-party processor — but on Shopify Advanced, ClickWerxs interchange-plus still saves money at volume. Off Shopify entirely, the surcharge disappears and savings typically run $200–$600/month at $50K/month. To reduce Shopify payment fees without leaving: upgrade your plan tier. To eliminate them: migrate your checkout and use interchange-plus pricing with no platform surcharge.
Staying on Shopify vs migrating your checkout changes the math entirely. Pick your situation.
If you're on Shopify Advanced ($399/month) and processing over $40K/month, ClickWerxs interchange-plus + the 0.5% surcharge can still beat Shopify Payments' 2.4% flat rate. The savings are smaller — but they're real, and you gain a dedicated account manager and next-day funding.
On Basic (2.0% surcharge) or mid-tier (1.0% surcharge), using ClickWerxs inside Shopify adds cost — not saves it. The surcharge makes any third-party processor uncompetitive on these plans. The math only works if you move your checkout off Shopify.
These features don't exist in any Shopify Payments plan. They come standard with a dedicated merchant account from ClickWerxs.
Shopify Payments charges a single flat percentage on every transaction. A $100 purchase on a regulated debit card and a $100 purchase on a premium rewards card both cost you 2.9% + $0.30. With interchange-plus, you pay the actual card network cost — debit at 0.05% + $0.21, premium rewards at 2.1% — plus a small fixed markup. The difference adds up to hundreds of dollars per month at volume.
Shopify support handles everything — storefront issues, billing questions, shipping integrations, and payment disputes — in one shared queue. When a payment hold or chargeback dispute lands, you wait. ClickWerxs assigns a named account manager to every merchant from day one. Direct phone, email, and text. They know your volume, your industry, and your history before you call.
Shopify Payments runs on a shared merchant ID. If Shopify adjusts its risk policies, updates its acceptable-use terms, or undergoes an ownership change, your processing can be affected even if you've done nothing wrong. A dedicated merchant account is yours — your direct relationship with an acquiring bank, your own underwriting file, your own account history.
Shopify Payments funds in 1–3 business days depending on your country. In Canada and some international markets, the standard is 3 business days. ClickWerxs provides next-day funding on all approved transactions as a standard feature — not a paid upgrade, not a feature reserved for high-volume merchants. Your sales from Monday are in your bank account on Tuesday. Cash flow is the oxygen of a business — you shouldn't wait three days for it.
“Shopify Payments works fine when you start. But once we hit $30K a month, the flat rate started costing us real money. We moved to ClickWerxs and our effective rate dropped almost a full point. That's $300 a month straight back into inventory. The account manager is the other thing — we had a chargeback dispute and it was handled in two days.”
“Shopify's surcharge on third-party processors is a trap. Migrating our checkout off Shopify was the right call — ClickWerxs interchange-plus pricing saved us $400/month immediately.”
Marcus D.
Fitness Equipment Retailer, Dallas TX
“I didn't realize Shopify Payments was an aggregator until my funds got held during a chargeback review. A dedicated merchant account from ClickWerxs gave me actual stability.”
Priya N.
Apparel Brand, Chicago IL
“We were on Shopify Advanced doing $80K/month. Switching to ClickWerxs saved $250/month on processing alone — plus next-day funding instead of two-day.”
Kevin T.
Home Goods Brand, Austin TX
“No one at Shopify support knew our business. Our ClickWerxs account manager does quarterly rate reviews and caught a downgrade pattern we didn't know about. Saved us $150/month.”
Diane F.
Beauty Subscription Box, Seattle WA
“High-risk product category — Shopify Payments wouldn't touch us. ClickWerxs reviewed our application individually and had us approved and processing in 36 hours.”
Tommy R.
Supplement Brand, Phoenix AZ
“Shopify's surcharge on third-party processors is a trap. Migrating our checkout off Shopify was the right call — ClickWerxs interchange-plus pricing saved us $400/month immediately.”
Marcus D.
Fitness Equipment Retailer, Dallas TX
“I didn't realize Shopify Payments was an aggregator until my funds got held during a chargeback review. A dedicated merchant account from ClickWerxs gave me actual stability.”
Priya N.
Apparel Brand, Chicago IL
“We were on Shopify Advanced doing $80K/month. Switching to ClickWerxs saved $250/month on processing alone — plus next-day funding instead of two-day.”
Kevin T.
Home Goods Brand, Austin TX
“No one at Shopify support knew our business. Our ClickWerxs account manager does quarterly rate reviews and caught a downgrade pattern we didn't know about. Saved us $150/month.”
Diane F.
Beauty Subscription Box, Seattle WA
“High-risk product category — Shopify Payments wouldn't touch us. ClickWerxs reviewed our application individually and had us approved and processing in 36 hours.”
Tommy R.
Supplement Brand, Phoenix AZ
Send your Shopify Payments statements. We'll calculate your effective rate, run the surcharge math for your plan tier, and show you exactly what you'd save with interchange-plus pricing.
Get a Free QuoteSide-by-side feature comparison, the surcharge math at your volume, and an honest take on when Shopify Payments is still the right choice.
ClickWerxs vs Shopify Payments