The Best Stripe Alternatives for E-commerce Merchants in 2025

Last Updated on November 19, 2025 by Ewen Finser

If you run an online store in 2025, there’s a good chance that Stripe is running your checkout. But as a CPA, I see many of my clients asking the same question:

“Is Stripe still worth the headaches… or is it time to move on?”

As it turns out, many merchants are quietly moving off Stripe in 2025 because of surprise fund holds, flat fees that creep up at scale, and support that feels like a black box. So with that in mind, I’ve put together a list of my top alternatives and why you should consider them.

TL;DR: If your pain is trust and visibility, a payments + ERP platform like Luqra or an enterprise option like Adyen gives you clearer risk management and better data. If your issue is cost or fit with your stack, Helcim, Shopify Payments, and Square often deliver lower effective rates or tighter platform integration without blowing up your checkout.

Why E-commerce Merchants Are Frustrated with Stripe in 2025

Stripe is still an impressive toolkit, powering everything from SaaS to marketplaces and developer-heavy shops. But if you sell physical or digital products online and live in the world of carts, AOV, and ROAS, its tradeoffs can be substantial.

1. Account Holds and Shutdowns

The single biggest complaint I hear isn’t about fees — it’s trust. You ship the product, Stripe processes the money… and then suddenly your payouts are delayed or frozen “for review.”

On Reddit, you see posts like “Stripe retaining funds with no resolution,” where merchants describe thousands of dollars in limbo while support sends boilerplate replies. When things like that happen, frustration doesn’t even come close to describing the feeling.

Stripe does have a formal complaint process and dedicated complaint channels, but from the merchant’s side, that still feels like you’re begging a black box to release your own money.

For an e-commerce brand with tight cash cycles, that is not a minor annoyance. That is payroll, ad spend, and the next inventory order.

2. Flat Rate Pricing That Slowly Stacks Up

Stripe’s standard online rate still centers around 2.9% + $0.30 per transaction, with extra markups for certain scenarios: manually entered cards, international cards, and currency conversion.

You can negotiate at scale, but for a lot of mid-market stores, you sit in the “not tiny, not huge” space and eat the rack rate.

3. Support and Communication

Stripe’s docs are world-class. Their reputation for support, on the other hand, is more mixed.

There are plenty of positive stories, but public complaints cluster around:

• Slow or canned responses when money is held
• Difficulty getting a clear explanation of “risk” flags
• The feeling that Stripe’s risk model is tuned for Stripe itself, not for merchants trying to meet payroll

If you’re running a serious e-commerce operation with tight cash flows, you may want a processor where you have a named human to escalate to — not just a ticket ID.

4. Complexity if You’re Not a Developer-First Shop

Stripe shines when you have developers who want to build a custom payments stack. It’s less friendly if you just want “cards, wallets, BNPL, and subscriptions that work, with reports my finance team can actually use.”

It’s possible to bolt together Stripe, a separate subscription tool, your e-commerce platform, and a BI stack. But every extra layer is another point of failure, another reconciliation issue, and another friction point when something breaks.

That is where some of the alternatives below are winning: they do fewer things, but they’re tuned for merchants, not just developers.

What to Look For in a Stripe Alternative

Before you jump ship, get clear on what matters for your store:

• Risk tolerance and underwriting: How are high-risk products handled? Are reserves and holds predictable, or does risk feel random?
  
• Payout speed and stability: Daily vs. weekly vs. “we’ll let you know.” You need to be able to depend on your cash and know when it will be available to you.
  
• Pricing model: Make sure you understand all your costs and compare them appropriately. Flat rate is simple. Interchange Plus can be cheaper if you have volume. Membership-style “pass-through” pricing can be cheaper still for the right profile.
  
• E-commerce platform fit: How well does the processor plug into Shopify, WooCommerce, BigCommerce, Magento, and other platforms in your stack?
  
• Chargeback and fraud tooling: You need strong fraud rules, not just declines for anything that looks weird. Adyen, for example, is now known for strong risk tools and chargeback management for e-commerce merchants.
  
• Data and analytics: You want to see which channels, SKUs, and payment methods are actually making you money. Luqra’s whole pitch, for example, is a unified payments + ERP + analytics layer.

With that in mind, let’s walk through the best Stripe alternatives for e-commerce merchants in 2025.

Luqra: Payments and an ERP for Merchants Who Care About Data

If Stripe is “payments as a developer toolkit,” Luqra is “payments as an operations and finance control center.” They combine merchant services with a payments-focused ERP and analytics layer, with the goal of unifying payment endpoints and the data around them — so you see the full life cycle of a transaction from checkout to bank.

From an e-commerce perspective, here’s what stands out:

• Unified payments and analytics: Instead of dumping Stripe exports into spreadsheets or a BI tool, Luqra gives acquiring banks, processors, ISOs, and merchants a single source of truth for payments data and reporting.
  
• ERP-style visibility: Luqra’s ERP manages everything from onboarding, compliance, and underwriting through to processing and payouts in one system. For merchants, that means fewer blind spots when something gets flagged as a risk.
  
• Near-real-time approvals and streamlined processing: Luqra’s docs emphasize near-real-time approvals to cut down delays and surprises in the payment flow.
  
• Support for different payment models: Luqra publishes best practices for subscription-based e-commerce, multicurrency, and a mix of cards, ACH, and wallets — which is often how DTC brands actually run.

Luqra is what I’d recommend if you’ve grown past “basic gateway” and you want payments, risk, and reporting handled in a way your finance and ops people can live with. If Stripe feels like a black box and your team is constantly exporting CSVs, Luqra is worth a hard look.

Helcim: Transparent Interchange Plus for Cost-Conscious Stores

Helcim is one of the clearest “Stripe but cheaper” options for many small to mid-sized merchants. Instead of flat-rate pricing, Helcim uses interchange plus, so you’re paying the actual interchange cost set by the card networks plus a fixed margin. As a result, you’re saving around 25% vs. flat-rate processors like Stripe and Square, especially as volume grows. On a store doing $500k, $1M, or $5M a year, that’s not “rounding error” money but a substantial boost to your net profit.

Here’s why e-commerce merchants like Helcim:

• Clear, published pricing: There’s no guessing which card types get surcharged and how much. You see the markup and know what you are paying for.
  
• Good fit for card-not-present: Helcim designs explicitly for both online and hybrid merchants, not just brick-and-mortar shops.
  
• Risk and chargebacks: Helcim charges a modest fee for chargebacks and will reimburse it if you win the dispute.

Helcim is not as “build anything you want” as Stripe, nor as full-stack ERP as Luqra. But if your main Stripe complaint is “the fees are killing me,” then Helcim deserves a spot on your shortlist.

Adyen: Enterprise-Grade Global Payments and Risk Management

Adyen is a global processor that sits upmarket from Stripe for many merchants. It powers large platforms and retailers and is especially strong with cross-border e-commerce, local payment methods, and marketplaces.

Here’s why e-commerce merchants move from Stripe to Adyen:

• Global and local payments in one contract: Adyen supports a large range of cards, wallets, and local payment methods through plugins for major e-commerce platforms.
  
• Built-in marketplace tools: Adyen for Platforms lets you onboard sellers, verify them, accept payments on their behalf, and control payouts. That’s why marketplaces and multi-seller platforms often default to them.
  
• Strong risk and chargeback management: Adyen’s risk engine and chargeback tools are known for reducing fraud and easing the pain of dispute handling for e-commerce merchants.

Adyen usually makes sense once you hit a certain scale or complexity, but if Stripe’s risk decisions are hurting your global expansion, it’s time to give it serious consideration.

Square: Simple, Omnichannel Payments for Smaller Stores

Square is often listed as a top Stripe alternative because it marries online payments with physical POS and hardware. SMBs love having everything under one umbrella, and Square excels at that. For e-commerce merchants who also sell at markets, pop-ups, or retail, that “one vendor for everything” approach is appealing.

Here’s where Square shines:

• Fast onboarding and low setup friction: You can start taking payments with a reader and enable simple online checkout very quickly.
  
• Good enough for small-catalog stores: If your catalog is not massive and you don’t have complex subscription or B2B needs, Square’s online tools are usually sufficient.
  
• Flat-rate simplicity: Like Stripe, Square charges flat-rate pricing. In fact, Helcim’s comparison table shows Square and Stripe in a similar range, a bit higher than Helcim’s interchange plus.

If your main need is “one simple vendor for cards both online and in person,” Square can replace Stripe without a big learning curve.

Shopify Payments: If You’re All-In on Shopify

If your store runs on Shopify, the easiest alternative to Stripe is probably Shopify Payments. This is Shopify’s built-in processor (which is actually powered by Stripe under the hood) that gives Shopify merchants a more integrated experience.

Here’s why Shopify Payments often beats the standalone Stripe vendor:

• No extra transaction fees: If you use third-party processors on Shopify, you pay an extra percentage on each sale. Using Shopify Payments usually removes those fees and often results in lower effective rates, especially on higher-tier plans.
  
• Fewer moving pieces: Payments, orders, refunds, and payouts all live inside the same dashboard. That makes life easier for your bookkeeper and your support team.
  
• Shop Pay: Shopify’s one-click Shop Pay checkout has huge adoption and conversion benefits, and it rides on top of Shopify Payments or compatible processors.

You’re still in Stripe’s world behind the scenes, but operationally, it feels different. If you’re already on Shopify and hate juggling systems, this is often the most frictionless “upgrade” path.

How to Pick the Right Stripe Alternative for Your Needs

If I were sitting down with you as your CPA and payments therapist, here’s the process I would use to pick a Stripe alternative:

1. Pull a real 12-month Stripe export: Look at volume, average ticket, card mix, and international share. That tells you how much an interchange plus model like Helcim could save vs. Stripe’s flat rate.
   
2. Map your actual risk profile: High-ticket, pre-order, and certain product categories will always look spicier to automated risk systems. If you’re already on the edge with Stripe, you need a partner who will talk through reserves and risk policy before a crisis hits. This is where Luqra or Adyen can be stronger fits.
   
3. Decide whether you need “just a gateway” or “payments ERP”
   • If you want deeper reporting, dispute workflows, and multi-entity or multi-brand visibility, Luqra gives you that ERP-style view.
   • If you only need a cleaner bill on the processing fees, Helcim and other interchange plus players are probably enough.
     
4. Run a pilot, not a blind jump: You do not have to rip Stripe out overnight. Many merchants stand up an alternative gateway on one store, channel, or region, then slowly rebalance volume once they trust the new partner.

If you’re still not sure, here’s a quick and dirty cheatsheet:

Stripe pain point	What you want	Alternatives to consider
Unpredictable holds, opaque risk	Clearer underwriting, better visibility	Luqra, Adyen
Fees eating into margins	Lower effective rates, interchange plus pricing	Helcim, (membership-style processors)
Weak support	Real relationships and named contacts	Luqra, certain boutique merchant acquirers
Need global/local methods & marketplaces	Strong platform tooling, many payment methods	Adyen
Middling support for Shopify	Embedded checkout, lower total cost of payments	Shopify Payments
Mediocre omnichannel capabilities	Simple setup across online + in-person	Square, Helcim

My Final Take

Stripe isn’t bad — it’s simply optimized for a different kind of customer than many 2025 e-commerce merchants have become. And the bigger your store gets, the more these quiet pain points start to matter.

But you don’t need to stay in a relationship where your cash flow, support, and data live at the mercy of a black box. In 2025, there are real Stripe alternatives built for merchants first, not just for developers.