Shopify Checkout vs Custom checkout

What it costs, plan tier by plan tier

Shopify Checkout has no price of its own. It comes with every Shopify plan, and the plan comparison on Shopify's pricing page shows where the cost really sits: the plan itself, card processing, and a 2% third-party transaction fee on the lower plans whenever a provider other than Shopify Payments takes the money. Any upsell or post-purchase app you install is billed on top.

A custom checkout is a second bill, next to the store or in place of its checkout. SamCart is the host most sellers price first. Core is $79 a month, and its pricing page lists 1-click upsells and order bumps on Pro at $199 a month. For a paid-traffic offer, Pro is the tier that counts, because those two features are why you would leave the native checkout in the first place. The SamCart review covers what else each plan adds.

ElasticFunnels starts at $97 a month on Starter, with every feature on every plan and limits set by page views. Its gateway fee applies only to revenue charged through gateways it runs, so a funnel that hands the buyer to Shopify for payment pays Shopify's costs on that sale and nothing extra to ElasticFunnels.

Add up the platform, the processing and the upsell app or plan tier at your own monthly volume, then set that against the revenue the bumps and upsells bring in. That total is the number to compare.

Shopify checkout limitations for paid traffic

Shopify's checkout is strong at the job it was built for. Shopify says Shop Pay can recognize 100M+ Shop Pay users by their email or device so they pay with one tap, and that one store's checkout handles up to 40,000 checkout starts a minute. In its own April 2023 study with a consulting firm, Shopify reports converting 15% better than competing platforms on average. That figure is Shopify measuring Shopify, and we found no independent test of one offer run on both kinds of checkout.

The limits appear once a media buyer wants the checkout to behave like a funnel step:

• Layout. The plan comparison marks checkout customization as Limited on every plan below Plus, and Plus is where Shopify advertises a fully customizable checkout.
• Upsells. Post-purchase pages, extra fields and tracking pixels arrive through checkout apps, and Shopify's checkout page labels those extensions as Plus features.
• Testing. Comparing two checkout designs means laying the checkout out twice, which the Limited setting below Plus does not allow.
• Processor choice. Bringing your own processor on a lower plan adds the third-party fee from the pricing section to that processor's own rate.

Checkout extensibility vs custom checkout

The two get mixed up because both promise a checkout of your own. Checkout extensibility is Shopify's way of adding to the checkout it hosts: apps insert blocks, fields, pixels and post-purchase pages, while the payment still happens on Shopify with Shop Pay and the store's stock in one system. A custom checkout moves the payment step itself onto a page you own, on your domain or a host such as SamCart, charged through your own gateway.

The choice comes down to where the payment happens. Extensibility suits a store that wants Shopify's checkout with a few extra parts. A custom checkout suits an offer whose margins depend on a bump before payment, an upsell page after it, and the freedom to test the checkout like any other page in the funnel.

A custom checkout page on Shopify

You cannot use one to replace the checkout on a Shopify storefront. Shopify's own App Store requirements tell app developers to use Shopify checkout. Merchants on r/shopify put it more bluntly: a reply in a thread about using an external checkout instead of Shopify's says third-party checkouts are no longer allowed and the store will get suspended, and another thread calls it against Shopify's terms. Those are merchant reports and carry less weight than Shopify's legal text, though the App Store rule points the same way.

Two setups keep the store and the funnel apart:

• Pre-checkout on your domain, payment on Shopify. The advertorial or lander lives in your funnel tool, and its buy button hands the cart to Shopify Checkout. You keep Shop Pay and the store's stock, and the checkout page itself stays Shopify's.
• A separate funnel with its own checkout. The ad points at a funnel on its own domain that charges through your gateway, with a bump and an upsell, and each paid order is then created in the Shopify store so the fulfilment apps ship it. The storefront keeps Shopify's checkout for everyone who shops the catalog.

The second setup is what this page means by a custom checkout for a Shopify brand, and it is the one that gives a media buyer control of the page that takes the money.

Where ElasticFunnels fits

ElasticFunnels is a funnel platform for teams running paid traffic. It builds the pages, with an AI builder that drafts a page from a prompt or clones one from a URL, hosts the checkout, and keeps sessions, orders, rebills and refunds on one timeline with a CRM and automations. Its lead feature is the one this decision turns on. Same-URL split testing rotates checkout variants on the server under one campaign link, so a checkout with a bump can run against one without while the ad keeps its address and its learning. The same-URL vs redirect testing comparison explains why that address matters on Meta.

For a Shopify brand it covers both setups above. Its checkout charges through Stripe, NMI, PayPal, Klarna or Authorize.net, with multi-MID routing across NMI accounts, or it can pass the buyer to Shop Pay and Shopify Checkout. When it takes the payment itself, its native order sync creates the paid order in the store with customer, SKU, shipping and tax, merges the main sale and its upsells into one Shopify order, and carries refunds across. The gaps are real: no product import from Shopify, synced orders leave Shopify stock untouched, tracking numbers do not flow back, and each store connects through a custom app set up with the ElasticFunnels team.

The larger drawback is how little outside evidence exists. ElasticFunnels is newer than the platforms it competes with and has very little independent review coverage, so until you run real volume through it you are mostly taking the vendor's word for its claims. That is what you would expect of a platform built since 2023, and it bears on how the claims hold at scale more than on what the features do. Pages, funnels and a custom domain can be set up on its 14-day trial without a card, which is enough to build the funnel before any spend moves to it. The ElasticFunnels review covers the rest of the platform, and ElasticFunnels vs CartFlows weighs it against the WooCommerce route.

My take

If the store sells a catalog and most revenue comes from returning customers, I would stay on Shopify Checkout, lean on Shop Pay, and add post-purchase offers through apps or Plus once volume justifies it. Rebuilding the checkout for that store adds a bill and a sync to watch for little gain.

If the business is one hero product sold on cold Meta or TikTok traffic, I would run a separate funnel with its own checkout, one bump and one upsell, and send each paid order into the store for fulfilment. I'd judge it on revenue per visitor over a full week of spend and leave the storefront on Shopify's checkout for everyone who arrives organically.

For the platforms that run that funnel, see the best checkout software roundup, CartFlows for WooCommerce, Checkout Champ vs CartFlows, all checkout comparisons and how we evaluate checkout tools.