If you sell in Mexico, Colombia, Argentina, or Chile, setting up your payment gateway is probably the most important technical decision you'll make for your store. And also one of the ones that generates the most errors.
I've seen it in dozens of stores in LATAM: owners losing sales every day because their gateway is misconfigured, because they haven't activated the payment methods their customers prefer, or because the checkout creates unnecessary friction that pushes the buyer to abandon.
In this guide, I'll explain how to integrate the three most used payment gateways in LATAM—MercadoPago, Conekta, and PayU—into your Shopify store, the most common errors you should avoid, and how to reduce cart abandonment due to payment issues.
Which payment gateway to choose based on your country in LATAM
Before diving into the configuration, you need to choose the right gateway for your market. Not all of them work the same in all countries, and not all offer the same local payment methods.
MercadoPago
The most versatile option for LATAM. Available in Mexico, Argentina, Colombia, Chile, Brazil, Uruguay, and Peru. Supports credit and debit cards, bank transfers, cash payments (OXXO in Mexico, Rapipago in Argentina), and interest-free installments. It's my first recommendation for stores selling in multiple LATAM countries.
Conekta
Specialized in Mexico. Supports cards, OXXO Pay, SPEI transfers, and cash payments at convenience stores. It has competitive commissions and a solid integration with Shopify. Ideal if you sell exclusively in Mexico and want an alternative or complement to MercadoPago.
PayU
Strong in Colombia, Mexico, Peru, Chile, and Panama. Supports local payment methods in each country: PSE in Colombia, OXXO in Mexico, PagoEfectivo in Peru. Widely used by medium and large companies that need to operate in multiple countries with a single integration.
Other relevant options by country
- Mexico: OpenPay, Clip, Kueski Pay (BNPL), Aplazo (BNPL)
- Colombia: ePayco, Wompi (from Bancolombia), Bold
- Argentina: Todo Pago, Oca
- Chile: Transbank, Khipu, Flow
For more information on payment providers available on Shopify, you can consult Shopify's official documentation on third-party payment providers here.
How to integrate MercadoPago in Shopify step-by-step
MercadoPago has official integration with Shopify through its app in the App Store. Here's the complete process:
Step 1: Create or verify your MercadoPago account
Before integrating, you need a verified MercadoPago account as a company or an individual with business activity. Verification requires uploading identification documents and, in some countries, tax information. Without full verification, you'll have collection limits.
Step 2: Install the MercadoPago app on Shopify
Go to the Shopify App Store and search for "Mercado Pago." Install the official app. You can also go directly to Settings > Payments in your Shopify admin panel and search for MercadoPago in the third-party payment providers section.
Step 3: Connect your MercadoPago account
The app will redirect you to MercadoPago to authorize the connection. Log in with your account and accept the permissions. Make sure to connect the correct account (production, not test) when you're ready to receive real payments.
Step 4: Configure payment methods
Within the app's settings, activate the available payment methods for your country:
- Mexico: Credit/debit cards, OXXO, bank transfer, interest-free installments (MSI)
- Argentina: Cards, transfer, installments with and without interest
- Colombia: Cards, PSE, cash
- Chile: Cards, transfer, WebPay
Step 5: Configure installments (critical for Mexico and Argentina)
If you sell in Mexico or Argentina, activating interest-free installments is one of the most important decisions you can make. I've seen it in dozens of stores: activating MSI (Meses Sin Interés) in Mexico can increase the average order value by 20% to 40%.
To activate MSI, you need a contract with participating banks through MercadoPago. The process can take a few days but is completely worth it.
Step 6: Make a test purchase
Before publishing, use MercadoPago's sandbox mode to make a complete test purchase. Verify that the payment is processed, that you receive the notification, and that the order appears correctly in Shopify.
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How to integrate Conekta into Shopify step-by-step
Conekta is an excellent option for stores selling exclusively in Mexico that want a solid integration with OXXO Pay and SPEI.
Step 1: Create your Conekta account
Register at conekta.com and complete the verification process. You'll need tax information for your company or business activity. The approval process can take 2-5 business days.
Step 2: Get your API keys
Once your account is approved, go to the Conekta panel and get your API keys: a public key and a private key. You'll have test (sandbox) keys and production keys. Use the test keys for configuration and the production keys when you're ready to receive real payments.
Step 3: Install the Conekta app on Shopify
Search for "Conekta" in the Shopify App Store and install the official app. You can also add it from Settings > Payments > Third-party payment providers.
Step 4: Enter your API keys
In the app settings, enter your public and private Conekta keys. Make sure to use the correct keys (sandbox for testing, production for real payments).
Step 5: Activate payment methods
Activate the available methods: credit and debit cards, OXXO Pay, and SPEI transfer. OXXO Pay is especially valuable in Mexico because it allows customers without a card to pay in cash at any OXXO store.
Step 6: Configure webhooks
Webhooks are automatic notifications that Conekta sends to Shopify when a payment is completed. It's critical to configure them correctly, especially for OXXO Pay where payment can occur hours after the customer generates the receipt.
How to integrate PayU into Shopify step-by-step
PayU is the preferred option for stores operating in Colombia and other LATAM countries simultaneously.
Step 1: Create your PayU account
Register at payu.com and select the countries where you want to operate. The verification process requires legal documents for your company and can take several business days.
Step 2: Obtain your credentials
PayU will provide you with a Merchant ID, an API Key, and an API Login. Keep this data securely; you'll need it for the Shopify configuration.
Step 3: Install the PayU app on Shopify
Search for "PayU" in the Shopify App Store. There are several apps available; make sure to install the official one or the most updated one with the best reviews for your specific country.
Step 4: Configure credentials and environment
Enter your Merchant ID, API Key, and API Login. Select the environment (sandbox for testing, production for real payments) and the country of operation.
Step 5: Activate local payment methods
Depending on your country, activate the available methods:
- Colombia: Cards, PSE (bank debit), cash (Efecty, Baloto)
- Mexico: Cards, OXXO, transfer
- Peru: Cards, PagoEfectivo, transfer
💡 Need to configure PayU for multiple countries or having trouble with integration? I have hourly packages for exactly these types of configurations. Check the options at yosoyexperto.com/precios.
Common errors when configuring payment gateways in Shopify (and how to avoid them)
These are the errors I most frequently see in LATAM stores:
Error 1: Leaving sandbox mode active in production
The most common and most costly error. The store is live, customers try to pay, but payments are not processed because the gateway is in test mode. Always verify that you are in production mode before publishing your store.
Error 2: Not configuring webhooks correctly
Webhooks are essential for deferred payments like OXXO or PSE, where the customer generates a receipt and pays hours later. Without correctly configured webhooks, Shopify doesn't receive payment confirmation, and the order remains in pending status indefinitely.
Error 3: Not making a complete test purchase
Many configure the gateway and assume it's good without making a real test purchase. Always make at least one complete transaction in sandbox mode and another in production with a minimum amount before opening the store to the public.
Error 4: Having multiple payment gateways misconfigured simultaneously
Having MercadoPago and Conekta active at the same time without a clear strategy can lead to confusion at checkout and technical conflicts. Define which is your primary gateway and which is the complement, and ensure both are well configured.
Error 5: Not verifying the gateway account before receiving payments
MercadoPago, Conekta, and PayU have verification processes that can limit the amounts you can collect or withhold funds if not completed. Complete the verification before you start receiving real payments to avoid surprises.
Error 6: Not clearly communicating available payment methods
If you accept OXXO, SPEI, or PSE but don't clearly communicate it in your store, many customers who prefer those methods will assume they're not available and abandon. Display the logos of accepted payment methods on the product page and in the footer.
How to reduce cart abandonment due to payment issues
Cart abandonment at the payment stage is especially frustrating because the customer has already decided to buy. These are the strategies I implement with my clients to reduce it:
Offer multiple payment methods
Not all your customers have a credit card or trust using it online. Offering OXXO, SPEI, PSE, or bank transfer can recover between 10% and 20% of abandonments due to a lack of a preferred payment method.
Activate Shop Pay
Shop Pay is Shopify's digital wallet. It allows customers to save their payment information and complete purchases with a single click. In stores with recurring traffic, it can increase the checkout conversion rate by 15% to 25%.
Display security seals at checkout
In LATAM, distrust of online payments is high. Displaying "Secure Payment" seals, gateway logos, and the SSL padlock visibly reduces friction when entering card details.
Set up abandoned cart recovery emails
Shopify has native abandoned cart recovery. Activate the automatic email that is sent 1 hour after abandonment. If you use Klaviyo, you can create more sophisticated flows with multiple touches.
Simplify checkout as much as possible
Every additional field at checkout is an opportunity for abandonment. Ask only for strictly necessary information. If you have Shopify Plus, you can customize the checkout to remove fields you don't need.
Frequently asked questions about payment gateways in Shopify for LATAM
Can I have MercadoPago and Conekta active simultaneously on Shopify?
Yes, it's possible to have multiple gateways active. However, you must ensure there are no conflicts at checkout and that the customer experience is clear. In most cases, one well-configured primary gateway is sufficient.
How much do MercadoPago, Conekta, and PayU charge per transaction?
Commissions vary by country and sales volume. As a general reference: MercadoPago charges between 2.9% and 3.99% + VAT per transaction in Mexico. Conekta between 2.9% and 3.6% + VAT. PayU varies by country. Always verify current rates directly with each provider.
How long does it take for sales money to be credited?
It depends on the gateway and your country. MercadoPago generally credits in 2-14 business days depending on the plan. Conekta and PayU have their own settlement cycles. Verify this before choosing your gateway, especially if you need quick cash flow.
What happens if a customer reports an unrecognized charge (chargeback)?
All three gateways have chargeback management processes. It's important to have documentation for each sale (order confirmation, shipping guide, customer communication) to dispute fraudulent chargebacks. MercadoPago offers seller protection in certain cases.
Do I need an RFC or RUT to use these gateways in Mexico or Colombia?
Yes. To receive payments legally and without limits, you need to be fiscally registered. In Mexico, you need an RFC; in Colombia, a RUT. Operating without fiscal registration can result in funds being withheld or account closure by the gateway.
Conclusion: the right gateway can be the difference between selling and not selling
In LATAM, where payment habits vary significantly between countries and where online distrust remains a real factor, choosing and correctly configuring your payment gateway is not a technical detail: it's a critical business decision.
A poorly configured gateway could be costing you sales every day without you realizing it. A well-configured one, with the correct payment methods for your market and without friction at checkout, can be one of the changes with the greatest impact on your conversion rate.
If you need help configuring your gateway, solving a technical problem, or evaluating the best option for your country and business model, I'm here.
Ready to have your payments working perfectly?
👉 yosoyexperto.com/precios — Choose your hourly package and let's resolve the configuration this week.
Or write to me on WhatsApp and tell me which gateway you are using and what problem you have. I'll respond within 24 hours.
