Best Business Bank Accounts for E-Commerce & Online Sellers: Shopify, Etsy, Amazon
Setting up a business bank account for your online store, whether it’s a new Shopify shop, an Etsy venture going full-time, or an Amazon FBA reseller, is a key step. The market for e-commerce-friendly banking has grown, but it can still be confusing. Four fintech banks stand out, each offering different perks for online sellers. Choosing wisely can save you time, transaction fees, and bookkeeping headaches for years.
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The Quick Answer
Novo for new or solo e-commerce sellers managing Shopify, Etsy, or Amazon payouts who need fast setup and easy integrations.
Relay for online stores needing to budget specific funds (inventory, ad spend, taxes) across multiple accounts or working with a bookkeeper.
Mercury for scaling e-commerce businesses with significant growth, external funding, or advanced treasury features as their transaction volume grows.
Brex for established, high-growth e-commerce brands with a team, large ad budgets, and a need for corporate cards and expense management.
Side-by-Side Breakdown
Mercury: $0/month. FDIC coverage $250K standard, $5M+ through sweep network. Best features: treasury management, API for custom financial reporting, team permissions. Best for funded e-commerce brands or high-volume online stores needing sophisticated tools.
Relay: $0/month (Pro $30/month). FDIC coverage $3M through program. Best features: up to 20 checking accounts (perfect for segregating funds for inventory, ad spend, and taxes), bookkeeper seats for easier collaboration on online store finances, team cards for contractors. Best for e-commerce businesses with complex cash flow or using a budgeting system like Profit First.
Novo: $0/month. FDIC $250K. Best features: fast setup for new online sellers, direct integrations with Stripe, Square, and Shopify for seamless payout tracking, easy invoicing for custom orders or wholesale. Best for solo e-commerce entrepreneurs, Etsy sellers, and new Shopify store owners.
Brex: $0 basic, varies for full platform. FDIC $6M+ through sweep. Best features: corporate cards for significant ad spend or bulk inventory purchases, expense management for remote teams, reimbursements for contractors. Best for established, venture-backed e-commerce companies with a growing team and high operational expenses.
When to Choose Mercury
Mercury shines when your e-commerce business starts scaling quickly, maybe after a successful funding round to expand inventory or marketing. If your online store processes high volumes of transactions, needs advanced ways to manage cash from different sales channels, or you’re dealing with international suppliers and want better treasury features, Mercury is a solid pick. Its clean interface and API can help custom track large inventory buys or complex payout structures.
When to Choose Relay
Relay is excellent for e-commerce entrepreneurs who like to keep their finances organized by purpose. You can easily set up separate checking accounts – one for your Shopify ad spend, another for Amazon FBA inventory purchases, one for tax savings, and even one for customer returns. This makes managing cash flow clear, especially if you use a system like Profit First for your online store. The bookkeeper seat also makes it simple for your accountant to access and reconcile transactions from different sales platforms without needing your login details.
When to Choose Novo
Novo is the go-to for new e-commerce sellers, Etsy shop owners, or solo Shopify entrepreneurs. It’s quick to set up and integrates directly with essential e-commerce tools like Stripe, Square, and Shopify, making it easy to track payouts and manage funds from your online sales. It’s genuinely free with no minimum balance, which is a huge plus for businesses just starting out or those with variable sales volumes. While great for solo operations, it's less suited for growing teams or businesses with complex financial needs.
When to Choose Brex
Brex becomes useful when your e-commerce brand is well-established, has a team, and is generating significant operational expenses. Think large ad budget spends on Facebook or Google, multiple employees managing inventory or customer service, or frequent business travel for product sourcing. Its corporate cards and integrated expense management can streamline tracking these costs. For a solo Etsy seller or a new Amazon FBA reseller, Brex's features are overkill – stick with Novo or Relay until your operations scale significantly.
The Verdict
For most new or solo e-commerce sellers, Novo offers the easiest start with crucial integrations. Relay is ideal for online stores focused on clear budgeting and managing cash flow for inventory, ads, and taxes. Choose Mercury when your e-commerce business is highly funded or scaling rapidly with complex financial needs. Brex is for established e-commerce brands with a team and significant expense management challenges. All are free to open, so starting with the best fit now will save you headaches later, even if switching is possible.
How to Get Started
All four banking options allow you to apply online in minutes. You'll generally need your Employer Identification Number (EIN) if you have one, your LLC formation documents (if applicable to your online store), and a government-issued ID. Mercury and Relay might have a short review period, especially for new e-commerce entities. Novo typically offers the fastest approval, getting your new online business bank account ready quickly. Pick the bank that best matches your e-commerce stage right now.
RECOMMENDED TOOLS
Mercury
Best business banking for funded startups and tech founders
Relay
Multi-account banking built for budget management and bookkeeper collaboration
Novo
Fast setup with Stripe, Square, and Shopify integrations
Brex
Banking, corporate cards, and expense management for venture-backed teams
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FREQUENTLY ASKED QUESTIONS
Are these real banks or fintech apps?
They are fintech companies that partner with FDIC-member banks to hold your deposits. Your deposits are FDIC-insured, but you are not banking directly with a chartered bank.
Can I use one of these and also keep a traditional bank account?
Yes. Many founders use Mercury or Relay as their primary operating account and keep a local credit union or Chase account for in-person cash deposits.
What if I am not approved?
Mercury and Relay can decline applications, often due to business type or state restrictions. Novo is generally more permissive. If declined, try another option or use a traditional bank while you build account history.
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