Running an online business is easier when payments are smooth and predictable. A merchant account connects your checkout, payment gateway, and payouts so you can get paid without friction.
The benefits of a merchant account include better tracking, faster access to funds, and a more trusted checkout. Genome offers merchant services built for modern online businesses. Learn all about merchant accounts in this article!
What is a merchant account?
A merchant account is a type of business account that helps you take customer payments and receive the funds in an organized way. With a merchant account, money from a purchase can move from the customer to your business, so you can get paid without manually tracking every transfer.
A merchant account is basically a gateway behind your checkout: when a customer pays, a payment processor handles the technical steps to confirm and route the payment. It is what makes online payments feel quick and simple for the buyer, while keeping your accounting cleaner on the business side. It’s also how businesses can accept credit cards and offer credit and debit card payments at checkout.
For customers, it’s convenient: they can pay using debit cards or other common methods they already trust. For businesses, it supports better cash flow by making incoming payments easier to track and reconcile. Many merchant account setups also pair with spending tools and financial services, like debit cards, for day-to-day expenses.
Genome’s merchant account is designed for modern EU-focused businesses that want a straightforward way to accept and manage payments in one place. Once your merchant account is live, you can focus more on sales and service, and less on finding ways to accommodate customers, as our services cover that!
How does a merchant account work?
A merchant account is the behind-the-scenes place where funds from customer transactions can be temporarily held and organized before they fully settle into the business bank account. At a high level, the flow is simple: you accept payments at checkout, the funds are authorized, and then they are settled into your main business account. Note that sometimes the money isn’t held there and is transferred to a company’s bank account.
Here’s the logic in plain terms. When a customer makes a purchase using online payments, the transaction is handled by a payment processor. The customer might pay via credit and debit card payments (so you can accept credit cards and accept credit and debit cards), and the system checks the customer’s credit account or available balance. In other cases, the funds come directly from the customer’s bank account. Once approved, the funds are recorded and held in your merchant account until they settle.
After that, settlement happens: the held funds are transferred into your business account, usually in batches or on a defined schedule. It is where a merchant account supports healthy cash flow, because it creates a predictable, trackable path from checkout to your operating funds. A second payment processor may be involved in routing, security checks, and confirmation steps.
There are different types of setups, from retail merchant accounts for in-person stores to online-first models. Some businesses may need a high-risk merchant account, depending on industry and transaction patterns. That’s why choosing the right merchant account provider matters: terms, timelines, compliance expectations, and support can vary across many merchant account providers.
In the EU, a modern merchant account experience can also be offered by electronic money institutions, like Genome. This approach can feel more integrated: settlement into a business account, clearer reporting, and easier connections to accounting software, all of which improve visibility and can boost customer satisfaction. In short, a merchant account acts as the bridge between customer payment activity and your business finances.
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in Genome online
Key benefits of using a merchant account
Accept payments professionally (online and in person). A merchant account helps you handle online payments and in-store checkout in a structured way, which is essential for online sales. It also makes it easier to offer modern options like contactless payments, so customers can pay how they prefer.
Build trust and upgrade the customer experience. When checkout feels familiar and smooth, people are more confident completing a purchase. A reliable flow reduces friction and strengthens the overall customer experience, especially for first-time buyers.
Reach a broader customer base. Payment preferences vary by market and by customer behavior. With the ability to accept credit cards, you remove a common barrier at checkout and make your business accessible to more buyers across channels.
Faster settlement to improve cash flow. A good setup shortens the gap between a sale and the money arriving in your business account, which can improve cash flow. That means fewer delays when you need to restock, pay suppliers, or invest in growth.
More reliable payment flows with EU-regulated accounts. Traditional structures often involve an acquiring bank and multiple intermediaries. In a modern EU model (like Genome’s approach), regulated digital account infrastructure can make payment handling clearer and more consistent.
Easier reconciliation and cleaner reporting. Transaction data is typically more organized, making it simpler to match payouts with invoices and orders. This reduces manual work and helps your team close books faster, with fewer mistakes.
More control over business finances. Instead of relying on workarounds like to carry cash, you gain better visibility into incoming funds, fees, and settlement timing. This supports smarter budgeting and day-to-day decision-making.
Lower payment processing risk with SEPA and Open Banking options. By reducing exposure to sensitive cardholder data and relying less on a single payment processor flow, businesses can diversify how they get paid and reduce operational risk, especially for recurring or high-volume payments.
Why merchant accounts are important for online businesses
Merchant accounts are important for online businesses because they turn online transactions into real, trackable funds your company can use. In e-commerce, they support fast checkout and fewer abandoned carts, helping you serve customers at any time, in any location. For SaaS and subscription-based models, a merchant account makes recurring billing more reliable, so renewals happen smoothly, and revenue is easier to predict. Digital services and fintech companies also benefit because payments need to be secure, automated, and easy to reconcile at scale.
Behind the scenes, a payment processor works with your setup to authorize and route electronic payments, while a payment gateway connects your website or app to that processing flow. Together, they help you accept credit and debit card payments without building complex payment infrastructure from scratch. The result is a simpler purchase experience for customers and more control, reporting, and consistency for your business as it grows.
Merchant account for subscription and recurring payments
A merchant account can be a strong fit for subscription products because it helps you manage recurring billing in a predictable, organized way. For many e-commerce businesses, SaaS tools, and digital services, subscriptions mean frequent online transactions that need to be confirmed quickly and tracked cleanly for renewals.
Today, Open Banking and SEPA-based recurring flows can be a modern alternative to credit card payments. Instead of relying on card details, customers can approve payments through their own bank with strong customer authentication (SCA). That makes electronic payments feel familiar and secure, while giving merchants clearer confirmation that a renewal has been initiated.
Genome is an example of this approach. It offers a merchant account so funds received from online payments can be used quickly, supporting smoother day-to-day business operations. Genome also enables Pay by Bank via Open Banking: at checkout, customers choose Pay by Bank, authenticate in their banking app, and once approved, funds move directly from the customer’s bank account to the merchant, often with fast confirmation and easier tracking for repeat renewals. We provide both SEPA Credit and Instant Transfers for this purpose.
How to choose a merchant account provider
To choose a merchant account provider, think like a small business owner who wants fewer payment headaches and more predictability. Start with regulatory status: a licensed, supervised provider is usually better equipped to protect funds and support compliant merchant services.
Next, check SEPA support, especially SEPA Credit and Instant, because it affects how quickly you receive payouts and handle transfers. If you sell online, ask about Open Banking features and how they connect to your checkout. Some providers support Pay by Bank, which can improve conversion and reduce failed renewals. Also, look at international transfers if you pay suppliers abroad or serve customers in multiple regions.
For subscriptions, see whether the provider offers an API and tools that fit recurring billing workflows, plus currency coverage if you operate in more than one market. Review available payment options, including how the payment gateway integrates and whether customers can still use debit cards.
Finally, compare onboarding, pricing, reporting, and support quality. The right provider helps you start accepting credit smoothly and deliver a seamless payment experience, backed by reliable merchant services.
Open an account
in Genome online
Why Genome is a modern merchant account for online businesses
Genome is a modern option for online businesses that want simpler, more reliable ways to process payments. As an EMI licensed by the Bank of Lithuania, Genome offers regulated merchant services built for today’s online economy, supporting both the business side (settlement, tracking, and reconciliation) and smoother checkout for customers.
One of the biggest benefits of a merchant account with Genome is that it can reduce payment failures compared to cards, which is especially helpful for subscriptions. With Open Banking payments (Pay by Bank), customers authenticate in their banking app, which can improve customer convenience and keep renewals more consistent.
We offer instant bank payments, allowing you yo accept SEPA Instant and Credit Transfers from customers. Card processing is coming soon as well.
Genome also supports B2B transfers, dedicated IBANs, and SEPA Credit & Instant, so funds can move quickly into your business checking account.
In practice, a merchant account ensures your incoming funds from online purchases are handled in a clear, regulated flow, with tools that support recurring revenue models. Genome’s merchant services are ideal for subscription businesses today, and payment processing of credit and debit card transactions is coming soon for merchants who want card acceptance alongside bank-based methods.
