Top Ecommerce Bookkeeping Firms in 2025 to Strengthen Your Online Business

Managing an online store is rewarding, especially in the USA, which is a thriving hub for ecommerce. But staying on top of your financials is a challenge many entrepreneurs face. Fortunately, in 2025, several top-tier bookkeeping firms are equipped to manage everything from daily transactions to strategic forecasting.

In this blog, we spotlight the top 10 ecommerce bookkeeping firms, each with distinct strengths to support your growth. Whether you’re scaling fast or just starting out, the right financial partner can make all the difference. Let’s help you find the perfect match for your ecommerce journey.

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Top 10 Ecommerce Accounting & Bookkeeping Firms in the USA

Choosing the right e-commerce bookkeeper is about finding a partner that blends expertise, flexibility, and cost-effective solutions. Firms like Ledger Labs, AccountingDepartment.com, Meru Accounting, Whiz Consulting, and Xendoo offer tailored accounting services designed to support online businesses of all sizes with scalable pricing and deep industry insight.

Ledger Labs

• Established in 2014, Ledger Labs has become a trusted accounting partner for e-commerce businesses across the US.
• Operates with a skilled team of 50–200 professionals dedicated to precision and scalability.
• Specializes in outsourced bookkeeping, virtual CFO services, ERP advisory, and tax planning.
• Highly experienced in platforms like Xero, QuickBooks Online, NetSuite, and Sage Intacct.
• Implements custom SQL-based automation tools for streamlined multi-platform integration.

Accounting Department.com

• Founded in 2004, the firm has grown into a recognized leader in remote accounting services.
• Employs over 200 full-time, US-based accounting professionals.
• Provides end-to-end outsourced accounting solutions for businesses of all sizes.
• Core services include bookkeeping, accounts receivable and payable management, CFO advisory, DCAA-compliant accounting, and cash flow forecasting.
• Primarily operates on QuickBooks Online and NetSuite for core accounting functions.
• Integrates additional tools such as Gusto, Jiray, and BQE Core for efficient operations and reporting.

Seller Accountant

• Founded in 2018, Seller Accountant is a boutique bookkeeping firm focused on e-commerce businesses.
• Operates with a small, specialized team of fewer than 25 professionals.
• Serves online sellers across major platforms such as Amazon and Shopify.
• Offers bookkeeping, catchup and cleanup services, tax compliance, financial reporting, and exit planning support.
• Utilizes tools like QuickBooks, Xero, and A2X for accurate financial tracking and automation.

Meru Accounting

• Established in 2013, Meru Accounting is a top-tier e-commerce accounting and bookkeeping firm serving clients across the USA.
• Employs a team of over 200 skilled professionals providing tailored financial solutions.
• Offers comprehensive services including bookkeeping, payroll, virtual CFO support, and tax filing.
• Specializes in software platforms such as Xero, QuickBooks, NetSuite, and A2X.
• Expertise includes inventory management, payment gateway tracking, accounts receivable and payable, payroll processing, and multi-channel sales reporting.
• Renowned for delivering accurate, tech-driven solutions customized for online and e-commerce businesses globally.

Whiz Consulting

• Founded in 2015, Whiz Consulting is a trusted accounting and bookkeeping firm serving businesses across the USA.
• Backed by a team of 100+ experienced finance professionals with diverse industry expertise.
• Offers comprehensive services including bookkeeping, accounts payable and receivable, financial reporting, inventory management, and sales tax compliance.
• Provides specialized support for multi-channel sales reconciliation and payment gateway tracking for e-commerce retailers.
• Skilled in accounting platforms such as QuickBooks, Xero, NetSuite, Zoho Books, and Microsoft Dynamics.
• Serves 100+ clients across the USA, UK, Australia, and UAE through an efficient offshore delivery model.
• Renowned for timely service, accuracy, and tailored financial solutions that support businesses of all sizes.

Monily

• Founded in 2002, Monily is a U.S.-based e-commerce accounting and bookkeeping firm headquartered in Houston, Texas.
• Employs a team of 51–200 professionals serving clients worldwide.
• Provides specialized e-commerce bookkeeping services for global online businesses.
• Offers bookkeeping, tax preparation, payroll, accounts payable and receivable, and outsourced CFO services.
• Experienced in integrating with major e-commerce platforms such as Amazon, Shopify, and Etsy.
• Utilizes leading accounting tools, including QuickBooks, Xero, and NetSuite for efficient financial management.

Xendoo

• Established in 2016, Xendoo is an e-commerce accounting and bookkeeping firm headquartered in Fort Lauderdale, Florida.
• Operates with a compact team of 11–50 professionals delivering accounting solutions for small online businesses.
• Provides services including bookkeeping, tax filing, catch-up accounting, and fractional CFO support.
• Seamlessly integrates with QuickBooks, Xero, A2X, Shopify, Amazon, and Stripe for efficient financial management.
• Known for its flat-rate pricing, quick onboarding process, and dedicated US-based customer support.
• Recognized as a reliable accounting partner for growing e-commerce brands seeking speed, accuracy, and simplicity.

InDinero

• Founded in 2009, InDinero has become a preferred financial partner for startups and e-commerce businesses seeking complete accounting solutions.
• Employs a large team of finance, tax, and strategy professionals offering integrated financial management.
• Provides a full suite of services including bookkeeping, tax preparation, financial planning, and CFO advisory.
• Specializes in multi-state e-commerce tax compliance and inventory cost tracking.
• Use a proprietary accounting platform along with integrations for QuickBooks, Shopify, Stripe, and Amazon seller systems.
• Known for delivering comprehensive, tech-enabled accounting support that scales with growing businesses.

Kruze Consulting

• Founded in 2013 by CPA Vanessa Kruze, Kruze Consulting caters primarily to venture-backed startups.
• Comprises a team of 100+ experienced accounting and finance professionals.
• Offers services in accounting, tax compliance, financial forecasting, and investor reporting.
• Works extensively with startup clients, including those in the e-commerce sector.
• Utilizes modern financial tools such as NetSuite, QuickBooks, Xero, Carta, and Stripe.
• Known for its tech-driven, scalable financial solutions tailored to high-growth businesses.

Kept.pro

• Established in 2020, Kept.pro is a US-based remote accounting firm focused on e-commerce businesses.
• Operates with a small yet skilled team of 11–50 professionals providing personalized financial support.
• Delivers a wide range of services including bookkeeping, accounts payable and receivable, payroll, financial reporting, and CFO advisory.
• Certified in QuickBooks Online and proficient with platforms like Shopify, A2X, Stripe, Gusto, and HubSpot.
• Recognized for combining technology and expertise to help online businesses maintain accurate, real-time financial visibility.

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Important Things to Consider Before Choosing an Ecommerce Bookkeeping Firm

While the firms listed above are among the top providers of ecommerce bookkeeping services, it’s essential to carefully evaluate your specific business needs before making a decision. Consider factors such as service scope, industry experience, pricing structure, technology capabilities, and the level of personalized support to ensure the firm aligns well with your operational goals and growth stage.

Consider the Services You Need

Your online business has unique financial complexities that go beyond standard bookkeeping. So, start your search with the kind and scale of ecommerce accounting services you require. Think about whether you need help with multi-state sales tax, marketplace fees (like Amazon or Etsy), inventory valuation, tracking COGS, and payment processing charges.

Ecommerce Experience

Not all bookkeeping firms are created equal when it comes to ecommerce. Seek out a firm with a demonstrable track record of working with online retailers. They should understand the nuances of the industry like tracking ecommerce KPIs, managing multi-channel sales, reconciling marketplace payouts, tracking inventory and COGS accurately. The industry experience will allow them to provide more insightful advice and accurate reporting specific to your online business performance.

Multi-State Sales Tax & Compliance Knowledge

E-commerce bookkeeping requires expertise in multi-state sales tax collection, payment, and filing, including nexus rules for tax obligations. Firms should also manage federal and state income tax preparation, estimated tax payments, and timely filing of Forms 1099- NEC for contractors. Staying compliant with evolving tax regulations is crucial to avoid penalties and ensure smooth compliance.

Technology & Integration

In ecommerce, tech is at the core, and your bookkeeping should match that pace. Look for a firm that uses accounting software like Xero, NetSuite or Zoho Books to integrate with your platforms, like Shopify, WooCommerce, or Amazon Seller Central. They should also connect smoothly with payment systems like Stripe, PayPal, and others. This setup helps automate entries, reduce manual errors, and give you real-time financial insights.

Transparent Pricing & Scalable Services

Choose a firm that’s upfront about pricing, no hidden costs, no surprises. As your ecommerce business grows, your needs will change. Make sure they offer flexible service plans that can scale with you. Whether you need basic ecommerce bookkeeping or advanced CFO support, the right firm should adapt. A dedicated remote bookkeeper can help you transition smoothly as you expand, offering consistent support at every stage.

Boost Profit Margins with Smarter E-commerce Bookkeeping Services

Choosing the right e-commerce bookkeeping firm in 2025 is crucial for online businesses aiming to thrive in a competitive market. Top firms combine specialized expertise, advanced technology, and a deep understanding of e-commerce platforms to deliver accurate financial management, tax compliance, and insightful reporting.

Whether you are a growing startup or an established brand, partnering with trusted e-commerce bookkeeping services ensures streamlined operations, better decision-making, and scalable growth, empowering your e-commerce business to succeed now and in the future.

Disclaimer:

This blog is intended for general informational purposes only. While every effort has been made to keep the content accurate and up to date, readers should verify the information independently or seek advice from a qualified professional before making any financial or business decision.