Top Ecommerce Bookkeeping Firms in 2025 to Strengthen Your Online Business

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Behind every successful online store lies a foundation of accurate, streamlined bookkeeping. In 2025, as digital commerce expands across platforms, currencies, and geographies, managing the financial back-end is more critical than ever. Top-performing e-commerce brands are turning to specialised bookkeeping firms that understand the pace and pressures of online retail, such as inventory fluctuations, payment gateways, and multi-channel reporting. In this blog, we highlight the leading e-commerce bookkeeping firms of 2025 that are trusted partners helping businesses stay compliant, profitable, and prepared for what’s next.

Top 5 Firms for Ecommerce Bookkeeping

In 2025, e-commerce businesses need financial experts who understand the fast-paced digital marketplace. Choosing the right partner can sharpen your financial edge, improve cash flow, and fuel growth. From real-time bookkeeping to tax compliance, and financial reporting and analysis, here are the top e-commerce accounting firms that offer scalable, tech-enabled solutions tailored to the fast-moving nature of the online retail industry.

1. Deloitte

Deloitte stands as a global leader in professional services, delivering robust ecommerce accounting and bookkeeping support for businesses operating across borders. Their key offerings include bookkeeping, tax compliance, financial reporting, and audit support, specifically tailored for ecommerce firms navigating complex international operations. With a presence in over 150 countries, Deloitte ensures regulatory compliance and consistency in financial practices worldwide.

2. PwC

PricewaterhouseCoopers (PwC) is among the top professional service firms, with operations in over 150 countries, including India. The firm offers end-to-end support in accounting, consulting, tax, and compliance services crucial for e-commerce businesses navigating global operations. Their core offerings include Tax, Audit & Assurance, M&A and Restructuring, Consulting, and Risk Advisory. With the growing demand for sustainability, PwC also leads in ESG advisory, guiding e-commerce clients to embed responsible practices and enhance sustainability reporting.

3. EY

Ernst & Young (EY) is one of the top professional service networks operating in over 150 countries. Within the ecommerce space, EY has emerged as a key player in providing end-to-end bookkeeping and financial support to online businesses. Their integrated structure helps ecommerce firms manage complex supply chains, cross-border transactions, and multi-channel revenue streams with ease. Moreover, through advanced digital platforms and accounting automation tools, EY enables more accurate, efficient ecommerce bookkeeping and real-time analytics.

4. KPMG

With a presence in over 140 countries, KPMG offers specialized services in audit, tax, and business advisory. In India, the firm supports e-commerce companies by streamlining bookkeeping processes and helping them stay compliant with local and international regulations. It also provides tailored insights into supply chain performance, inventory control, and financial reporting. To address growing digital risks, KPMG actively strengthens its cybersecurity and data privacy frameworks, a critical support for e-commerce businesses managing sensitive data.

5. BDO USA, LLP

BDO USA is part of a global network but focuses heavily on serving mid-sized businesses. Their core services include Assurance, Tax, and Advisory, tailored to the needs of growing ecommerce firms. Moreover, the company offers ecommerce bookkeeping solutions that integrate modern accounting technology, improving accuracy and financial visibility. Their experience in sectors like technology and healthcare, both closely linked to ecommerce, enhances their ability to support fast-moving businesses. BDO’s consistent service delivery is supported by strong internal processes and a stable workforce, ensuring reliable support for ecommerce clients scaling their operations.

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Fast-Growing e-Commerce Accounting Firms to Watch in 2025

Besides the globally established accounting firms as mentioned above, there are thriving companies that provide effective and tailored solutions for ecommerce firms of different sizes. Here is the list of bookkeeping firms that offer versatile services, flexible pricing models, and reliable support.

1. Whiz Consulting Private Limited

Whiz Consulting has been offering outsourced accounting services to US-based ecommerce businesses for 10+ years. Their goal is to offer tech-enabled ecommerce bookkeeping services built around client needs. With over 100+ accountants onboard, the firm offers a wide range of e-commerce bookkeeping services, including inventory tracking, reconciliations, AP/AR management, and sales tax compliance.

Moreover, each client also gets a dedicated ecommerce bookkeeper, ensuring focused support and better communication. Industry expertise combined with a technology-driven approach ensures accuracy, speed, and compliance at every step.

2. Mindspace Outsourcing Services Pvt. Ltd.

Mindspace Accounting Outsourcing Services has clients across the US and the UK. They’ve built a solid reputation in outsourced accounting and ecommerce bookkeeping over the years. Their services cover bookkeeping, tax prep, financial reporting, and even virtual CFO services.

For ecommerce businesses, they offer access to skilled remote bookkeepers who handle daily accounting with precision. What makes them stand out is their strength in financial analysis and project management. This means clients get clear, timely insights and a smooth workflow, essential for fast-paced ecommerce operations.

3. Indinero

Indinero is a remote-first US company that focuses on delivering full-service financial solutions for ecommerce brands. Headquartered in Los Angeles, they also operate in Indiana and Oregon. They offer ecommerce bookkeeping, tax filing, financial statements, and CFO-level insights, all in one place.

What makes Indinero stand out is its blend of tech and people. Clients work with a dedicated remote bookkeeper while also accessing advanced tools for real-time tracking. For ecommerce firms managing multi-state or cross-border operations, Indinero offers seamless support that scales with the business.

4. Hiline

Hiline, based in Syracuse, NY, specializes in outsourced accounting services for small businesses, with a strong focus on ecommerce. They support over 300 clients across the US, offering ecommerce bookkeeping, CFO services, tax strategy, HR and payroll, and spend management. Every client is matched with a remote bookkeeper who ensures accuracy and timely updates.

Their strength lies in Hiline OS, a platform that integrates people, tools, and workflows. This system gives online stores better control over e-commerce cash flow and financial planning.

5. Graphite (Graphite Financial)

Graphite Financial, founded in 2016 and based in New York, serves fast-growing ecommerce startups across the U.S. They offer a wide range of services, including ecommerce bookkeeping, accounts payable management, invoice processing, tax filing, financial modeling, and fractional CFO support. Every client is assigned a dedicated remote bookkeeper who handles daily accounting tasks and reporting.

Their team also helps with fundraising prep and setting up the right financial tech stack. This would help ecommerce founders access the right technology to streamline their existing processes and mitigate errors.

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

Ecommerce often means selling across states, and sometimes across borders. That brings complex tax rules into play, which may be beyond the scope of a standard bookkeeper. Your bookkeeping firm should understand multi-state sales tax compliance and keep up with changing regulations. Additionally, they must know how to handle tax collection, filing, and reporting across different jurisdictions.

Technology & Integration

In ecommerce, tech is at the core, and your bookkeeping should match that pace. Look for a firm that uses accounting software built 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, has no hidden costs and 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.

Final Word

The 2025 ecommerce bookkeeping landscape is rich with options. From the global reach of the Big Four to the agile efficiency of outsourcing partners, each offers unique strengths. What matters most is alignment between your business and the financial partner. Choose a provider of ecommerce bookkeeping services who truly understands your sales channels, platforms, and reporting requirements. The right firm balances your books, uncovers valuable insights, flag risks early, and empowers smarter financial decisions.