ClickWerxs vs Shopify Payments: Dedicated Merchant Account vs Aggregator
2.9%+30¢
Shopify Basic flat rate
2.0%third-party
Shopify Basic surcharge
$15
Shopify chargeback fee
$0
ClickWerxs surprise holds
Quick Answer
Shopify Payments is a payment aggregator, not a dedicated merchant account. It charges a flat rate of 2.4%–2.9% with no interchange-plus option, and adds a 0.5%–2.0% surcharge on any third-party processor you use instead. A dedicated merchant account from ClickWerxs uses interchange-plus pricing, gives you your own merchant ID, next-day funding, and a dedicated account manager. On Shopify Advanced processing $40K+/month, ClickWerxs saves money even with the surcharge. Off Shopify entirely, savings start around $15K–$20K/month.
ClickWerxs vs Shopify Payments: Feature Comparison
Side-by-side across pricing model, support, funding speed, and account stability. Where Shopify Payments wins, we say so.
Pricing Model
Online Processing Rate
In-Person Processing Rate
Third-Party Processor Surcharge
Dedicated Merchant Account (own MID)
Next-Day Funding
Dedicated Account Manager
Chargeback Fee
High-Risk Industry Support
Cash Discount / Surcharge Programs
Account Hold Policy
Month-to-Month Contract
Level 2/3 B2B Data Support
eCommerce Platform Required
Shopify Payments rates from shopify.com/pricing, accessed June 2026. ClickWerxs rates vary by merchant profile and processing volume.
The Surcharge Trap Most Merchants Don't See Coming
Shopify Payments is built to keep you inside the Shopify ecosystem. Use a third-party payment processor — including ClickWerxs — and Shopify charges an additional fee on every transaction: 2.0% on Basic, 1.0% on Shopify, 0.5% on Advanced (shopify.com/pricing). That surcharge adds to whatever your processor charges. On most plans, that makes ClickWerxs more expensive to use inside Shopify than Shopify Payments — not because our rates are higher, but because Shopify penalizes you for using a dedicated merchant account.
- Shopify Basic: 2.0% surcharge on all third-party processor transactions
- Shopify mid-tier: 1.0% surcharge — narrows the savings gap significantly
- Shopify Advanced: 0.5% surcharge — interchange-plus can still win at high volume
- Shopify Plus: 0.15% surcharge — effectively zero; savings kick in around $250K/month
- Leaving Shopify entirely eliminates the surcharge — and is often cheaper at scale
Effective Rate on $50K/month — Online Sales
Avg interchange assumed 1.8%. Actual rates vary by card type and volume.
What Shopify Payments Costs vs ClickWerxs at Real Volume
$290
Extra/month on Basic
At $10K/month: Shopify Basic (2.9%) = $290. ClickWerxs off Shopify (avg 1.9%) = $190. Shopify's 2.0% surcharge erases savings if you stay on Basic.
$400
Saved/month off Shopify
At $50K/month: Shopify Payments Advanced (2.4%) = $1,200. ClickWerxs merchant account (avg 1.9%) = $950. Savings: $250/month, $3,000/year — without the surcharge.
0%
Surcharge off platform
When you process through ClickWerxs outside of Shopify — on your own checkout, invoices, or POS — Shopify's surcharge does not apply. You pay interchange-plus only.
$15
Shopify chargeback fee
Shopify charges $15 per chargeback dispute. ClickWerxs includes dispute management support with every merchant account, handled by your dedicated account manager.
When Shopify Payments Is the Right Choice
We believe in honest comparisons. Shopify Payments makes sense in these situations — know when to stay.
- You're on Shopify Starter or Basic and process under $5K/month — the flat rate is fine at low volume
- Your entire business runs inside Shopify and you value the native dashboard integration
- You have no immediate need for a dedicated account manager or high-risk underwriting
- You accept Shopify's automated dispute handling and $15 chargeback fee as reasonable
- You're an early-stage merchant and the instant approval with zero paperwork is your priority
- You operate in a country where ClickWerxs doesn't yet have local acquiring relationships
What a Dedicated Merchant Account Gives You That Shopify Payments Can't
These aren't marginal differences — they're structural advantages that only exist with a true dedicated merchant account.
Your Own Merchant ID
Shopify Payments pools your transactions with thousands of others under a shared MID. You have no direct relationship with the acquiring bank. ClickWerxs gives you your own MID — your own banking relationship, your own underwriting, your own statement.
Interchange-Plus Transparency
Shopify Payments offers no interchange-plus option at any tier. You pay 2.4%–2.9% flat, regardless of whether the card costs 0.05% or 2.1% at interchange. ClickWerxs shows every card network cost on your statement — no bundling, no hiding.
A Person, Not a Dashboard
Shopify Payments support routes through the same queue as your storefront issues. ClickWerxs assigns a dedicated account manager from day one — direct phone, email, and text access to someone who knows your business.
No Automated Holds
Payment aggregators — including Shopify Payments — can hold your funds based on automated risk signals. Chargebacks, volume spikes, or a change in your product mix can trigger holds without notice. ClickWerxs never freezes funds without a direct conversation first.
Cash Discount Programs
Shopify Payments has no mechanism for passing processing fees to customers. ClickWerxs offers compliant cash discount and surcharge programs that can eliminate your processing costs entirely — legal in most US states and Canadian provinces.
Processing Beyond Shopify
ClickWerxs processes payments wherever you sell — physical retail, invoices, phone orders, your own checkout, POS terminals. Shopify Payments only works inside the Shopify ecosystem. One merchant account, everywhere you do business.
“We were on Shopify Advanced paying 2.4% plus the subscription. When we migrated to a custom checkout and ClickWerxs, our effective rate dropped to 1.7%. That's over $300 a month we were losing. The dedicated account manager alone was worth it — somebody who actually picks up the phone.”
How to Switch from Shopify Payments to a Dedicated Merchant Account
The process depends on whether you stay on Shopify or migrate your checkout. Both paths are straightforward.
Decide: Stay on Shopify or Migrate Your Checkout
If you stay on Shopify, you'll pay Shopify's third-party surcharge (0.5%–2.0% depending on plan). If you're on Advanced or Plus, ClickWerxs can still save you money. If you're on Basic or Shopify mid-tier, migrating your checkout to a custom storefront is the path to full interchange-plus savings.
We'll run the math with your actual volume and plan cost to show you which path saves more before you decide anything.
Request a Free Statement Analysis
Send your Shopify Payments statements from the last 3 months. We calculate your effective rate, project your ClickWerxs cost (with and without surcharge), and show exact monthly savings. No commitment required.
Most analyses are delivered within 2 business hours.
Apply for Your Merchant Account
Submit your business details and processing history. ClickWerxs underwriting typically approves merchant accounts within 24–48 hours. Your dedicated account manager handles the paperwork.
Configure Your Payment Gateway
For Shopify merchants staying on the platform: your account manager configures your ClickWerxs gateway as a Shopify-compatible third-party processor. For merchants on a custom checkout: we integrate with your existing stack or connect through our standard integrations.
Run Both in Parallel, Then Cut Over
Keep Shopify Payments active during the transition. Process a few test transactions through ClickWerxs, confirm the statement is clean, then switch your default. Your Shopify transaction history remains fully accessible.
Most merchants complete the full cutover in under a week with zero downtime.
Frequently Asked Questions: Shopify Payments vs Dedicated Merchant Account
See Your Exact Savings vs Shopify Payments
Send your Shopify Payments statement — or just tell us your monthly volume and plan. We'll calculate your effective rate, run the surcharge math, and show you whether staying on Shopify or migrating saves more.