How to secure payments on marketplaces

Online marketplaces bring together buyers and sellers in one place, and your payment process holds the entire experience together. A single weak link can disrupt trust or reduce revenue. Many merchants are working across countries, currencies, and products, which makes secure payments on marketplaces a priority. The goal is to create a payment flow that feels smooth while guarding against the risks that come with multi‑party transactions.

What marketplace payments are

Marketplace payments differ from standard e‑commerce because funds rarely move from one buyer to one seller directly. Instead, you manage a shared environment with several moving parts. You guide the buyer to pay through your platform, then distribute the funds to the correct seller while keeping your commission.

A typical structure includes:

• A payment gateway to capture the transaction.
• A processor to authorise and route the payment.
• A settlement layer to move funds to each seller.
• A clear fund‑flow model that handles commission and payout splits.
  
  

In most cases, the flow looks like this: the buyer pays through your platform; the platform receives the funds; the seller receives the payout; the platform keeps the agreed share. You may also support refunds, partial refunds, holds, or reserves, which add further responsibility to your payout and reconciliation processes.

Key risks to payments on marketplaces

Fraud-related risks

Fraud remains the most visible threat. Buyer-seller collusion, account takeover, and multi-party fraud appear often in high-volume environments. Global losses from online payment fraud surpassed USD 44.3 billion in 2024, and estimates expect this to reach more than USD 100 billion by 2029. Regions differ in exposure. 

Latin America reported the highest loss proportion at 4.1% of e-commerce revenue, while Asia Pacific reached 2.6%. Refund and policy abuse also became one of the most common attack types in 2024. Many merchants now report fraud-related costs above USD 10 million each year.

Regulatory and compliance risks

You also face regulatory and compliance risks. These include misaligned merchant of record structures, weak data protection, or gaps in payments regulation. Each jurisdiction comes with its own requirements for handling personal data, conducting due diligence, and managing AML checks.

Operational and reputational risks

Operational and reputational risks form another group. Chargebacks can lead to financial exposure, and inconsistent dispute handling can damage trust. 

Seller defaults may also delay payouts or leave you responsible for refund liabilities. If buyers or sellers feel uncertainty around your payment process, confidence drops quickly.

Core security principles for marketplace payments

Data protection

Data protection plays a central role. Encryption and tokenisation keep payment information secure in transit and at rest. Many of you follow PCI DSS as a baseline standard. Strong authentication helps prevent unauthorised access. When sensitive files move between systems, you may rely on secure channels such as SFTP and RSA-based signing.

Identity checks and verification

KYC, KYB, and AML controls help you verify buyers and sellers. These checks give you confidence that your marketplace interacts with legitimate participants. They reduce the risk of fraud and support compliance in regions with tight financial regulations.

Escrow and delayed payouts

Escrow or delayed payout structures protect both sides where trust is still forming. Holding funds until you confirm delivery or until disputes clear can support a safer environment.

Chargeback and dispute management

Chargebacks and disputes need careful management. Clear evidence collection, timely response, and fair treatment across all parties help you maintain order and reduce financial loss.

Best practices for securing marketplace payment workflows

Securing marketplace payments requires thoughtful choices in technology and process.

• Use a unified payment gateway with multi-party fund splitting to keep your workflow consistent and reduce manual steps.
• Offer multi-currency and local payment options to reduce cross-border decline risk and support buyer familiarity.
• Apply strong fraud prevention and risk scoring that can detect unusual activity and adapt to changing behaviour.
• Strengthen identity verification for merchants and payout recipients with automated onboarding flows.
• Maintain compliance across jurisdictions, including data protection, AML rules, and local tax obligations.

Advanced marketplace security features

The next wave of marketplace payment solutions brings opportunities and new responsibilities.

• Real-time payments and instant payouts improve seller cash flow while demanding faster monitoring and risk checks.
• Open banking expands secure payment options and requires strong API security to safeguard access.
• AI and behavioural analytics help identify suspicious activity early and support quicker decision-making.
• Tokenisation and biometric authentication reduce the exposure of raw payment data and limit unauthorised access.

Managing seller onboarding and payout security

Seller onboarding forms one of the most important steps in securing marketplace payments. Automated KYC and KYB flows reduce friction while maintaining accuracy. You gather the right information upfront and apply consistent checks for each new seller.

Split payment models protect both the platform and sellers. These models help you manage commission, refunds, and cost allocations transparently.

Settlement controls and clear reconciliation processes support accurate payouts. When sellers can see how fees, commissions, and payouts align with each order, they gain trust in the platform.

Refunds, reserves, and holds help you manage dispute risk, especially during peak seasons or when working with new sellers. Transparent rules help keep expectations clear.

Conclusion

Securing payments on a marketplace means creating a payment platform that protects data, confirms identity, and manages funds with care. You balance speed with safety and support cross‑border growth with consistent controls. If you choose to work with external partners, look for those who offer multi‑party fund splitting, strong risk scoring, and simple onboarding flows. Providers like Antom can support these goals while giving you the flexibility to process payments across regions with confidence.