Best Payment Gateways for QuickBooks Desktop Pro

Find and compare the best Payment Gateways for QuickBooks Desktop Pro in 2026

Use the comparison tool below to compare the top Payment Gateways for QuickBooks Desktop Pro on the market. You can filter results by user reviews, pricing, features, platform, region, support options, integrations, and more.

  • 1
    EBizCharge Reviews
    Top Pick

    EBizCharge

    EBizCharge

    $25/month
    207 Ratings
    See Software
    Learn More
    EBizCharge stands at the forefront of integrated B2B payment gateway solutions, facilitating secure online transactions for more than 400,000 users throughout the United States and Canada. Our payment gateway enables businesses to accept online payments securely while seamlessly syncing transaction data with over 50 different ERP, CRM, and accounting platforms. With EBizCharge, the online payment process is revolutionized, simplifying e-commerce transactions, removing the need for duplicate entries, minimizing payment failures, and enhancing the overall checkout experience. Our gateway offers robust features including secure online credit card processing, API integrations, hosted payment pages, tokenization, real-time processing capabilities, fraud prevention measures, and detailed reporting. EBizCharge adheres to PCI compliance standards and employs sophisticated data encryption and tokenization techniques to safeguard all online payment information. Additionally, EBizCharge effortlessly integrates with popular platforms such as QuickBooks, NetSuite, SAP, Oracle, Sage, Microsoft Dynamics, Salesforce, Acumatica, among others.
  • 2
    Nickel Reviews
    Top Pick
    We built Nickel because the systems businesses use to move money tend to profit in ways nobody can see. So we publish the economics behind every product we sell, something no other payment processor does, and it's why 25,000+ B2B companies and the accounting firms serving them now run money through us. On collections, branded links and hosted portals let clients settle invoices by card, ACH, or paper check with nothing to sign up for. On disbursements, an email address is all we need to send funds by ACH, card, wire, or physical check, routed through whatever approval rules your team defines. Costs stay low by design: ACH carries no fee and no volume ceiling, our Core tier bills nothing monthly, chargebacks cost you zero, and domestic cards run a flat 2.9% that can be shifted onto whoever is paying. Each transaction lands in QuickBooks matched line by line, and unused funds accrue 2% APY inside Nickel Balance. Setup runs about five minutes and needs no card.
  • 3
    PayTraQer Reviews
    Top Pick

    PayTraQer

    SaasAnt Inc

    $9/month/user
    11 Ratings
    PayTraQer automates the sync of your sales, fees and refunds from popular ecommerce platforms like Amazon, Shopify and eBay. It also reconciles these data in QuickBooks, Xero and BigCommerce. PayTraQer syncs fees, online payments and other transactions between QuickBooks, Xero, and Xero, as well as Paypal, Stripe and Square. It also syncs Clover, Pin Payments and Authorize.Net. PayTraQer automates accounting and streamlines the process of integrating e-commerce with Xero or QuickBooks for accurate, real-time synchronization. Say goodbye to manual data input and hello to efficiency. Features: Automated Data Extraction Robust Integration Multi-Channel Support The User Experience is Intuitive Customization Options Manage Multiple Currencies Real-time Insights Hassle-free tax compliance
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