Top 10 Accounting & Billing Providers for 3PLs (2026)

Rails is a SaaS platform that consolidates and fully automates financial operations such as client billing and supplier bill reconciliation for fulfillment 3PLs. 3PLs using Rails have seen savings of 20+ accounting labor hours, eliminated billing errors to the tune of 10% of the total invoice amount, and sent out bills within hours of the billing period ending while previously having taken days to do so. Users have also improved profitability by efficiently implementing dynamic client billing agreements, and identified lost revenue by reconciling carrier bills and charging clients for adjustments automatically. Rails integrates with a 3PL’s existing WMS, carriers, and accounting system through one-click integrations and brings in data as it is recorded in each system to enable real-time billing and reconciliation. Rails primarily works with 3PLs offering small-parcel fulfillment services such as outbound shipping (including services such as FBA), storage, etc. of all sizes (from 100 orders/month to 100,000+ orders/month). The only requirement is that the 3PL use a WMS for recording operations

40Seas is a fintech startup dedicated to transforming cross-border trade finance with innovative, digital-first solutions. Their platform provides small and medium-sized importers and exporters a modern substitute for traditional B2B payment and financing methods. By leveraging data-driven technology, 40Seas simplifies cross-border trade processes, offering faster, cost-effective access to working capital. This empowers businesses to enhance cash flow, boost sales, and expedite growth without depending on conventional financial institutions. Committed to rewriting the rules of trade finance, 40Seas is positioned as a best-in-class provider in the financial services industry.

A2X is a specialized accounting automation platform founded in 2014 that streamlines financial reconciliation for eCommerce businesses. Based in Auckland, New Zealand, with a team of 51-200 employees, A2X focuses on solving the complex challenge of accurately reconciling sales data from marketplaces and payment processors with accounting systems. The platform automatically categorizes and matches sales transactions, fees, taxes, and deposits to provide clean, audit-ready books in popular accounting software like QuickBooks Online, Xero, Sage, and NetSuite. What sets A2X apart is its deep understanding of eCommerce accounting complexities, particularly around marketplace fees, multi-currency transactions, and tax compliance across different jurisdictions. The platform transforms what typically takes hours of manual reconciliation work into an automated process that delivers accurate financial statements and detailed reporting on profit margins, COGS, and channel performance. This makes A2X an invaluable tool for 3PLs managing multiple client accounts and eCommerce brands seeking to maintain accurate financial records while scaling their operations.

Automate your billing with Margin. Create invoices with net terms and metered billing. Automatically reconcile carrier label costs to protect margins. Set custom charge rules so you bill exactly how you want. Provide clients with a transparent dashboard to see charges and download invoices. Consult directly with Cat (former 3PL operator) for strategies to fix cash-flow strain. Fix your cash flow today.

Avalara is a leading provider of cloud-based tax compliance automation software, serving businesses of all sizes across multiple industries since 2004. With headquarters in Durham, North Carolina, and over 4,500 employees, the company specializes in simplifying complex tax calculations, filing, and compliance processes for sales tax, VAT, GST, and customs duties. Their comprehensive platform integrates seamlessly with over 1,400 business systems including ERPs, eCommerce platforms, and point-of-sale solutions. For 3PL operators and eCommerce brands, Avalara eliminates the complexity of managing tax compliance across multiple jurisdictions and channels. Their automated solutions reduce manual errors, ensure regulatory compliance, and scale with business growth, making them particularly valuable for companies operating in multiple states or countries with varying tax requirements.

Bill.com is a comprehensive financial operations platform that transforms how businesses manage accounts payable, accounts receivable, spend management, and expense tracking through AI-powered automation. Founded in 2006 and headquartered in San Jose, California, the company serves over 400,000 businesses with its unified platform that seamlessly integrates with leading accounting software to streamline financial workflows. With features ranging from automated bill processing and approval workflows to intelligent expense categorization and cash flow optimization tools, Bill.com eliminates manual financial tasks while providing real-time visibility into business finances. For 3PL operators and logistics companies, Bill.com offers particular value through its ability to handle complex multi-vendor payment scenarios, automated invoice processing for numerous suppliers, and integrated spend management capabilities. The platform's AI-enhanced automation reduces processing time by up to 50% while improving accuracy, making it ideal for logistics businesses dealing with high transaction volumes from freight carriers, warehouse suppliers, and service providers. Additionally, Bill.com's credit facilities and The BILL Divvy Card provide flexible financing options to help 3PLs manage cash flow fluctuations common in the logistics industry.

Octup is the first platform to unite warehouse intelligence with billing automation. Built for 3PLs, Octup is the industry’s most complete billing solution, automating invoicing, capturing missed billables, applying complex rate cards accurately, and enabling more frequent billing to get paid faster.

Portal Warehousing provides flexible and scalable warehousing solutions across various US locations including Brooklyn, Phoenix, Orlando, Los Angeles, and Salt Lake City. They specialize in offering high-quality small to medium-sized warehouse spaces that cater to businesses ranging from startups to large enterprises. With no long-term lease commitments, their turn-key spaces come equipped with essential amenities including private offices, superb security, and super-fast internet. Additionally, Portal Warehousing supports business growth through a host of services like community events, growth support, reception services, and technology partnerships. They also provide easy monthly billing, shipping and receiving addresses, utilities, and daily carrier pickups. By reimagining warehousing, Portal Warehousing ensures enterprises can focus on their growth with convenience and ease. They operate on a flexible membership structure, allowing businesses to choose from a range of access levels and corresponding fees, aligning perfectly with diverse operational needs and providing a collaborative environment to foster growth and innovation. Their mission centers on redefining the warehousing experience to elevate and support business operations through comprehensive, adaptable services.

QuickBooks Commerce is an integrated e-commerce accounting solution that bridges the gap between online selling platforms and financial management. As part of Intuit's QuickBooks ecosystem, it automatically syncs e-commerce data from multiple sales channels into QuickBooks, providing real-time visibility into revenue, expenses, and profitability. The platform eliminates manual data entry by connecting directly with popular marketplaces and e-commerce platforms, while intelligently separating fees, taxes, and actual revenue. What sets QuickBooks Commerce apart is its deep integration with the QuickBooks accounting platform and its ability to provide automated payout reconciliation. The solution automatically matches marketplace payouts with bank deposits, accounting for platform fees and taxes, which significantly reduces the complexity of multi-channel financial management. With built-in reporting and cash flow insights, it enables businesses to make data-driven decisions while maintaining accurate books for tax compliance and business analysis.

TaxJar is a Boston-based sales tax compliance platform founded in 2013 that specializes in automating complex tax calculations and filings for e-commerce businesses and 3PLs. With coverage across 11,000+ tax jurisdictions, the company helps businesses navigate the intricate landscape of sales tax compliance, from economic nexus monitoring to automated filing and remittance. What sets TaxJar apart is their focus on multichannel commerce, offering AI-driven product categorization, real-time tax calculations, and seamless integrations with major e-commerce platforms like Amazon, Shopify, and WooCommerce. Their flexible API also enables custom integrations with ERP systems and warehouse management platforms, making them particularly valuable for 3PLs managing tax compliance across multiple clients and sales channels.

Xero is a leading cloud-based accounting software platform that has been transforming financial management for businesses since 2006. Founded in Wellington, New Zealand, Xero offers comprehensive financial solutions designed to streamline accounting processes, automate routine tasks, and provide real-time business insights. The platform serves as an all-in-one financial hub, enabling businesses to manage everything from invoicing and expense tracking to payroll and inventory management through a secure, cloud-based interface. What sets Xero apart in the accounting software landscape is its emphasis on automation and integration capabilities. The platform connects with over 1,000 third-party applications, making it particularly valuable for logistics and supply chain businesses that need to sync financial data with warehouse management systems, shipping platforms, and e-commerce tools. With features like automated bank reconciliation, intelligent invoice processing, and customizable reporting dashboards, Xero helps 3PLs and logistics companies maintain accurate financial records while reducing manual administrative overhead.

Your Shipping Partners (YSP) gives 3PLs and shippers direct access to enterprise-level carrier rate cards across USPS, FedEx, DHL, and Amazon - pricing typically reserved for national providers. YSP is already integrated into existing WMS systems, and automatically applies discounted rates at shipment creation without having to change carriers. Clients ship as usual, pay as they go, and reduce shipping costs by 10–25% or more as volume scales, without operational disruption.