Resource Center

Top 3 Payments Software for Retailers and eCommerce

Payments Software is used to move and reconcile money among shippers, intermediaries, carriers, and service providers. For retailers and ecommerce, this can be a specialized need rather than a core daily workflow. The work may instead belong to a customer, partner, or another team. Compare the listed details with your needs and confirm current capabilities with providers.

At a glance: Payments Software for Retailers and eCommerce

Stripe, Billtrust, Freightos Marketplace are three product options to compare for Retailers and eCommerce in Payments Software. Review their listed details below. A detail that is not listed may still be available, so ask providers about your requirements.

Product profiles

Stripe

Financial infrastructure for payments, invoicing, and treasury. Profile fit: Tech-enabled logistics companies; Profile fit: Marketplaces and platforms; Profiled strength: Best-in-class APIs; Profiled strength: Global payment coverage.

Details to compare

  • feature: Invoicing
  • feature: Subscription billing
  • integration: QuickBooks
  • integration: Xero
View full product profile

Billtrust

Order-to-cash automation for invoicing, payments, and cash application. Profile fit: Enterprises with high invoice volumes; Profile fit: Companies needing AR automation; Profiled strength: End-to-end order-to-cash; Profiled strength: AI-powered cash application.

Details to compare

  • feature: E-invoicing
  • feature: Online payment portal
  • integration: SAP S/4HANA
  • integration: Oracle ERP
View full product profile

Freightos Marketplace

NASDAQ-listed freight marketplace with 1.3M+ transactions and 67 carriers. Profile fit: SMB importers and exporters; Profile fit: E-commerce and Amazon FBA sellers; Profiled strength: NASDAQ:CRGO with 1.3M+ transactions annually; Profiled strength: 67 carriers covering 66% of world air cargo market.

Details to compare

  • feature: Instant Quotes
  • feature: Rate Benchmarking
  • integration: SAP ERP
  • integration: Oracle TMS
View full product profile

Compare product details

Listed fieldStripeBilltrustFreightos Marketplace
FeaturesPayment processing, Invoicing, Subscription billing, Connect marketplace payments, Treasury services, Card issuing, Fraud prevention, Global payments, Developer APIs, Financial reportingE-invoicing, Online payment portal, AI cash application, Credit management, Collections automation, Payment acceptance, EDI integration, ERP connectivity, Analytics and reporting, Customer self-serviceInstant Quotes, Rate Benchmarking, Multi-Modal Booking, Real-Time Tracking, Carbon Tracking, Document Management, Payment Processing, FBX/FAX Indices, HS Code Finder, Route Analyzer
IntegrationsNetSuite, SAP, QuickBooks, Xero, Shopify, WooCommerce, BigCommerce, Magento, Salesforce Commerce Cloud, PrestaShop, Shop-Ware, Celigo, Dell Boomi, Zapier, Oracle Opera, Mirakl, CommercetoolsSAP, SAP S/4HANA, Oracle ERP, Microsoft Dynamics 365, Microsoft Dynamics GP, Microsoft Dynamics NAV, NetSuite, Acumatica, Sage Intacct, Sage X3, Infor, EpicorSAP ERP, Oracle TMS, project44, FourKites, Payoneer, ShipBob, Amazon FBA, Alibaba.com, Google Cloud, REST APIs
SubcategoriesFreight Payment and Settlement PlatformsFreight Payment and Settlement PlatformsPayment Platforms / Freight Wallets
Buyer-fit detailsTech-enabled logistics companies, Marketplaces and platforms, Businesses needing modern payment infrastructureEnterprises with high invoice volumes, Companies needing AR automation, B2B businesses accelerating collectionsSMB importers and exporters, E-commerce and Amazon FBA sellers, Enterprise shippers with API needs
Target company sizesstartup, smb, mid-market, enterprisemid-market, enterprisesmb, mid-market

Not seeing a capability here? Ask the provider whether it is available for your needs.

What to consider for Retailers and eCommerce

For retailers and ecommerce, this category may support an adjacent or specialized need rather than a core daily workflow. Its usefulness depends on the work involved and whether it complements an existing system.

  • Payment initiation and approval
  • Remittance and transaction status
  • Reconciliation, exceptions, and controls

Questions to ask vendors

  • How does each listed capability—such as Payment processing or Invoicing—work in your actual retailers and ecommerce process?
  • What setup, data access, responsibilities, and support would be required to use Payments Software with your existing systems?

Payments Software for retailer ecommerce buying guidance

At a glance: Freight payment workflows connect transportation invoices and supporting records to review, approval, disbursement, remittance and accounting reconciliation. Separate workflows may cover international transfers or driver disbursements. The payment method, timing, currency, fees, controls and responsibilities depend on the specific provider, financial institutions and transaction. Freight Audit and Payment Services; Freight Expense Accounting; Freight Solutions for Shippers; Freight Solutions for Brokers; ACH Payments Fact Sheet; Tips for Originators to Comply with 2026 Risk Management Rules; 49 CFR 371.3 — Records to be kept by brokers

Fit for retailer ecommerce (conditional)

A retailer may use freight payment for inbound transport, store replenishment or 3PL invoices; parcel refunds, marketplace payouts and customer payments are separate scopes. Freight Audit and Payment Services; Freight Solutions for Shippers

Workflow: Separate each charge stream and payee, link invoices to the relevant shipment or purchase order and preserve route-specific terms. Freight Audit and Payment Services; Freight Solutions for Shippers

Ask in a demo: Trace an inbound freight invoice and store-delivery charge separately through review and payment. Freight Audit and Payment Services; Freight Solutions for Shippers

Check before choosing: Do not assume a freight payment workflow covers ecommerce checkout, returns or marketplace settlement. Freight Audit and Payment Services; Freight Solutions for Shippers

Common workflows

  • Transportation invoice settlement: Receive and link an invoice to shipment and rate records, review exceptions, approve the amount, pay the correct party and reconcile remittance. Cass and Triumph describe freight-specific payment and invoice workflows; confirm the service and handoff in the buyer's contract. Freight Audit and Payment Services; Freight Solutions for Shippers; Freight Solutions for Brokers
  • Payment-rail and settlement review: Compare eligible payment methods, cutoffs, fees, returns and funds availability for the actual payer and recipient. Nacha describes ACH options, including Same Day ACH conditions and banking-day settlement; it does not establish timing for every freight payment. ACH Payments Fact Sheet
  • Broker transaction records: Keep the required transaction data and payment record within the broker's own procedure. The current eCFR text of 49 CFR 371.3 includes specified information on freight charges collected and the date of payment to the carrier; this is a limited legal reference, not advice. 49 CFR 371.3 — Records to be kept by brokers

Questions to ask providers

  • Which parties, invoice types, modes, payees, currencies and payment corridors are included?
  • How are invoices matched to shipment IDs, contracted rates and supporting documents?
  • What payment methods, cutoffs, fees, limits, funding and return terms apply to our transaction?
  • How are payee or bank-detail changes independently verified and approved?
  • Who reviews an exception, authorizes release and owns a failed or misdirected payment?
  • How do remittance details reconcile to our TMS, ERP, bank and carrier records?
  • What audit evidence and exports are available to the payer, carrier and other authorized parties?
  • Which regulatory or recordkeeping responsibilities remain with our organization?

Frequently asked questions

Are freight audit and freight payment the same workflow?

No. Audit examines charges and records; payment transfers funds after approval. A provider may offer both. Cass describes invoice validation, audit and payment as related but identifiable service functions. Freight Audit and Payment Services

Does ACH always settle on the same day?

No. Nacha describes Same Day ACH for eligible payments and settlement on banking days. Confirm eligibility and timing with the financial institutions and provider. ACH Payments Fact Sheet

Can a platform guarantee a carrier's payment date?

Do not assume a universal date. Check the written cutoffs, funding, processing, recipient institution, return and contract terms for the specific payment. Freight Audit and Payment Services; ACH Payments Fact Sheet

What should a broker's payment record contain?

The current text of 49 CFR 371.3 specifies broker transaction fields including collected freight charges and carrier-payment date. Confirm current applicability with qualified counsel or the regulator. 49 CFR 371.3 — Records to be kept by brokers

How should a buyer handle a payee change?

Use an independently verified contact path and documented approval rather than relying only on a change request; verify the roles and controls demonstrated by the provider. Freight Audit and Payment Services; Freight Solutions for Brokers; Tips for Originators to Comply with 2026 Risk Management Rules

Can one platform support cross-border and domestic freight payments?

Do not infer this from a product label. Confirm the exact currency, corridor, beneficiary, rail, fees, returns, timing, invoice match and remittance terms in writing. Freight Audit and Payment Services; Freight Solutions for Shippers

Sources (7)
  1. Freight Audit and Payment Services — Cass Information Systems
  2. Freight Expense Accounting — Cass Information Systems
  3. Freight Solutions for Shippers — Triumph
  4. Freight Solutions for Brokers — Triumph
  5. ACH Payments Fact Sheet — Nacha
  6. Tips for Originators to Comply with 2026 Risk Management Rules — Nacha
  7. 49 CFR 371.3 — Records to be kept by brokers — Electronic Code of Federal Regulations / FMCSA

Buying guide for Retailers and eCommerce · Technology guide · Category listings · Resource Center