Choosing the wrong payment gateway for your Shopify store isn't just a technical issue: it's money lost along the way. Unexpected fees, customers abandoning their carts because you don't accept OXXO, chargebacks you can't dispute, and deposits taking two weeks to clear. All of that eats into your profit margin.
In Mexico, the payments landscape is more complex than in other markets: a predominantly debit-based economy, a culture of interest-free installments that can increase your average order value by up to 50%, and 10% of shoppers who only pay in cash at OXXO convenience stores. The payment gateway you choose determines how many of these shoppers you can captureβand how much it costs you to do so. This article compares Shopify Payments, MercadoPago, Conekta, Stripe, and PayPal using real-world data.
73%
37% of Mexicans have a bank account, but only 37% have a credit card
Debit cards are the most common online payment method in Mexico β your payment gateway should be optimized for that.
Source: CNBV / INEGI, National Survey of Financial Inclusion 2021
In this article
1. The Payments Landscape in Mexico
Before entering the payment gateways, you need to understand the context in which they operate. The online payments market in Mexico has four characteristics that make it radically different from other markets:
Debit rules, not credit.
With only 37% credit card penetration, the vast majority of your customers will pay with debit. Debit fees are different (and generally lower) than credit fees. Ignoring this means projecting inaccurate margins.
OXXO is a real source of income
Cash payments via OXXO represent approximately 10% of online transactions in Mexico . This isn't a marginal nicheβit's a segment of shoppers with real purchasing power who simply don't have (or don't want to use) a card. If your payment gateway doesn't natively support it, you're missing out on that 10%.
Interest-free installments (MSI) increase your average ticket price.
Installment plans are a cultural expectation in Mexico, not a bonus. Mexican shoppers are used to seeing "3, 6, 12 installments" on any significant purchase. Offering installments can increase your average order value by 30% to 50% because shoppers are more willing to spend when the cost is spread out. Without installments, you're competing with one hand tied behind your back.
Chargebacks in Mexico are the highest in Latin America.
Mexico has a chargeback rate of 2.81% , the highest in Latin America. This is no small detailβit means you need a payment gateway with robust fraud protection, a clear dispute process, and Spanish-language support that understands the local context.
SPEI and BNPL are growing: SPEI transfers are gaining ground β with no interchange fee for the seller. BNPL solutions like Kueski Pay and Aplazo are also expanding in Mexico and can increase conversion rates on high-value items.
2. Shopify Payments
Shopify's native payment gateway. If you qualify in Mexico, it's the first option to consider for a simple reason: it eliminates Shopify's additional commission on third-party transactions (see section 8).
Transaction fees
3.3 β 3.5%
Credit/Debit Card
+ $3 MXN
Fixed fee per transaction
Exact rate according to plan (Basic, Shopify, Advanced)
β Advantages
- β No extra Shopify transaction fees
- β Native integration β no complex configuration required
- β Direct dispute management in the panel
- β Deposits in 2-5 business days
- β Fraud protection included (Shopify Protect)
β Disadvantages
- β No native support for OXXO Pay
- β Limited MSI β depends on issuing banks
- β No 24/7 phone support in Spanish
- β Possible account blocking in "high-risk" businesses
Best for: Stores that primarily sell by card (no urgent need for OXXO) and want the simplest integration without additional Shopify fees.
3. MercadoPago
MercadoLibre's payment gateway is the most widely used in Latin America . In Mexico, it stands out for its ecosystem, which includes OXXO convenience stores and MercadoPago account balances. It's a solid option for broad and diverse audiences.
Transaction fees
2.95%
Debit card
3.49%
Credit card
+ $4 MXN
Fixed fee per transaction
OXXO Pay: Additional fee for cash transactions (see current rates)
β Advantages
- β Native OXXO Pay β accepts cash
- β High brand trust in LATAM
- β Accepts MercadoPago account balance
- β MSI available with participating banks
- β Support in Spanish
β Disadvantages
- β Variable deposit times: 2-14 days
- β Shopify extra commission (0.6-2%) applies
- β Dispute protection can be slow
- β Less polished reporting interface than Stripe
Best for: Stores with a broad audience in Mexico that need to accept OXXO and have a customer base that already uses MercadoLibre or has a MercadoPago account.
4. Conekta
A 100% Mexican company, regulated by the CNBV. It is the only payment gateway on this list built specifically for the local market β with OXXO, SPEI, and MSI integrated from the start, not as add-ons.
Transaction fees
3.4%
Credit/Debit Card
+ $3 MXN
Fixed fee per transaction
OXXO and SPEI have specific rates available on their official websites. See Enterprise plans for high-volume transactions.
β Advantages
- β Native and integrated OXXO Pay
- β SPEI / supported bank transfers
- β MSI available with all major banks
- β Specialized support in Spanish (local team)
- β Deposits in 2-5 business days
β Disadvantages
- β Shopify extra commission (0.6-2%) applies
- β Lower brand recognition than MercadoPago
- β Dashboard and less advanced reporting tools
Best for: Stores that need to accept OXXO, SPEI and MSI with local support in Spanish, especially if they value working with a Mexican company regulated by the CNBV.
5. Stripe
The industry standard for developer experience. For stores with advanced technical requirementsβcustom flows, subscriptions, marketplacesβStripe is hard to beat. Its key limitation for Mexico: no native OXXO integration .
Transaction fees
3.6%
Credit/Debit Card
+ $3 MXN
Fixed fee per transaction
SPEI available as an additional method. Deposits in 7 business days (longer than competitors).
β Advantages
- β Best developer experience on the market
- β Very comprehensive analytics and reporting dashboard
- β Radar (anti-fraud with machine learning)
- β Subscriptions and advanced billing
- β Accepts SPEI and multiple international methods
β Disadvantages
- β No native OXXO Pay
- β 7-day deposits (the slowest in the comparison)
- β Shopify extra commission (0.6-2%) applies
- β Support in Spanish with variable response times
Best for: Stores with dedicated developers, advanced technical requirements, or businesses that also sell in international markets where OXXO is not relevant.
6. PayPal
The most internationally recognized brand in this comparison. It has a considerable installed base in Mexico, especially in cross-border transactions. However, it has the highest fees on this list , and its dispute resolution process tends to favor the buyer.
Transaction fees
3.95%
Credit/Debit Card
+ $4 MXN
Fixed fee per transaction
Instant deposits available to PayPal accounts. Bank transfers may take an additional 1-3 business days.
β Advantages
- β Increased brand confidence globally
- β Instant deposit to PayPal account
- β Ideal for international sales / export
- β One-click purchase for users with an account
β Disadvantages
- β Highest commission in the entire comparison
- β Without OXXO Pay
- β Dispute process frequently favorable to the buyer
- β Shopify extra commission (0.6-2%) applies
- β Possible withholding of funds on new accounts
Best for: Stores that sell to international customers or have a customer base that prefers PayPal, but not as the primary payment gateway if you operate only in Mexico due to its high fees.
7. Complete Comparative Table
All the data side by side in a single view:
| Feature | Shopify Payments |
Market Pay |
Conekta | Stripe | PayPal |
|---|---|---|---|---|---|
| TDC Commission | 3.3β3.5% | 3.49% | 3.4% | 3.6% | 3.95% |
| TDD Commission | 3.3% | 2.95% | 3.4% | 3.6% | 3.95% |
| Fixed fee | $3 MXN | $4 MXN | $3 MXN | $3 MXN | $4 MXN |
| OXXO Pay | β No | β Yes | β Yes | β No | β No |
| MSI | Limited | β Yes | β Yes | Limited | β No |
| SPEI | β No | β No | β Yes | β Yes | β No |
| Deposit time | 2β5 days | 2β14 days | 2β5 days | 7 days | Instant* |
| Anti-fraud | β Included | β Included | β Included | β Radar | β Included |
| Support in Spanish | Partial | β Yes | β Local MX | Partial | β Yes |
| Shopify extra commission | β None | 0.6β2% | 0.6β2% | 0.6β2% | 0.6β2% |
*PayPal: instant to PayPal account; bank transfer, 1-3 additional days. Approximate percentages β check current rates on each platform.
8. Shopify's Extra Commission Explained
The most surprising thing to see when reviewing your statement is that if you use any payment gateway other than Shopify Payments , Shopify charges an additional fee per transactionβon top of what the gateway already charges. Here's how it works:
How much does Shopify charge for using third-party payment gateways?
Basic Plan
2%
per extra transaction
Shopify Plan
1%
per extra transaction
Advanced Plan
0.6%
per extra transaction
Specific example: Basic Plan + MercadoPago, sale of $1,000 MXN :
The difference adds up: With a $100,000 MXN/month Basic Plan + MercadoPago, you pay approximately $5,890 MXN in fees. With Shopify Payments, it would be approximately $3,380 MXNβ $2,510 MXN less per month , or $30,120 MXN per year in your pocket.
9. Which one to choose according to your case
The answer depends on your business model, audience, and volume. Here are recommendations for each scenario:
New store, first ecommerce, no OXXO needed.
Recommendation: Shopify Payments
The simplest setup, with no extra Shopify fees, built-in fraud protection, and deposits in 2-5 days. If you qualify in Mexico, it's the logical starting point.
Broad audience, mass consumer products
Recommendation: MercadoPago (+ Shopify Payments in parallel)
Capture 10% of OXXO shoppers and regular MercadoLibre users. Activating both is the most complete combination if the plan allows it.
Maximum coverage of payment methods in Mexico
Recommendation: Conekta
Native OXXO, SPEI, full MSI, and local team support. Ideal for broad audiences where cash and transfers are common.
Advanced technical development, subscriptions, or marketplace
Recommendation: Stripe
With dedicated developers and support for custom flows or advanced billing, Stripe's API is unmatched. Slower deposits and a higher fee are justified by the technical flexibility.
International sales or customers who prefer PayPal
Recommendation: Use PayPal as a secondary, not primary, payment gateway.
It makes sense if you sell to the US or Europe, or if your shopping cart analytics show buyers prefer it. As the only payment gateway in Mexico, its fees are hard to justify.
A winning strategy for most: Shopify Payments as the primary payment gateway (with no extra fees) + MercadoPago or Conekta as an alternative for OXXO. This combination covers the vast majority of payments in Mexico without sacrificing profit margin.
At Marketon, we evaluate each client's business model before recommending the payment gateway combination. Technical setup is included in the delivery of your custom Shopify store.
Do you need help setting up your payment gateways?
At Marketon, we configure Shopify Payments, MercadoPago, Conekta, and more as part of our custom Shopify store. Fixed price, 20 business days delivery, no surprises.
Sources
- Shopify Help Center β Shopify Payments Mexico Rates (2025)
- MercadoPago, Conekta, Stripe, PayPal β Official rates Mexico (2025)
- CNBV / INEGI β National Survey of Financial Inclusion 2021
- Americas Market Intelligence β Digital Payments LATAM 2024
- Cybersource / Visa β Global Fraud and Chargeback Report LATAM
- AMVO β Online Sales Study Mexico 2024