Running a successful DTC (Direct-to-Consumer) ecommerce business means balancing creativity, marketing strategies, and logistical challenges — yet behind the scenes, solid bookkeeping is what keeps the operation seamless.

Ecommerce bookkeeping isn’t just about recording numbers; it’s about understanding the flow of money to make informed decisions, avoid costly mistakes, and maximize profitability.

Whether you’re a new ecommerce business owner or a seasoned entrepreneur, this guide will also cover how doola Bookkeeping can streamline your finances so you can stay focused on growth.

How Is Ecommerce Bookkeeping Different From Traditional Bookkeeping?

Ecommerce bookkeeping requires a tailored approach that addresses the unique complexities of online sales.

Here’s a quick comparison to highlight the key differences between traditional and ecommerce bookkeeping:

Feature	Traditional Bookkeeping	Ecommerce Bookkeeping
Transaction Consistency	Generally consistent with predictable patterns	High variability due to online promotions, flash sales, and returns
Sales Tax	Straightforward with single-location application	Complex, often requiring multi-state compliance
Inventory Management	Less intensive; simple tracking	Dynamic, impacted by seasonality and multi-channel stock levels
Transaction Fees	Usually limited or minimal	Varies widely by platform (e.g., Amazon, Shopify fees)
Technology Integration	Often limited to basic accounting software	Requires integration across multiple sales channels and payment processors

For ecommerce businesses, these added layers demand specialized tools and expertise — making doola Bookkeeping the ideal partner to help manage these complexities seamlessly.

Book a demo to learn how doola can help with ecommerce bookkeeping.

7 Common Ecommerce Bookkeeping Mistakes to Avoid

Even seasoned bookkeepers face unique challenges in the ecommerce space.

Here are seven common challenges that ecommerce businesses encounter — and tips to counter them.

1. Not Having a Clear View of Your True Income

Ecommerce income isn’t just a sum of sales.

It involves deductions for returns, refunds, discounts, merchant fees, and sales tax. Ignoring these can create an inflated view of profitability.

Example:

Let’s say you receive a $500 deposit from a platform like Shopify or Etsy.

While it might seem like $500 in income, it could actually represent $600 in gross sales, offset by $50 in returns, $30 in merchant fees, and $20 in discounts.

Plus, $25 of that amount might be sales tax that you owe to the state — not profit.

Without consistently accounting for these details, you could end up with a bloated view of your profitability that doesn’t align with reality, leading to potential financial missteps.

2. Incorrect Gross Margin Calculations

Gross margin is a vital metric, especially in ecommerce, but it often gets miscalculated when costs like merchant fees, packaging, and shipping are left out.

Example:

Let’s say there’s an ecommerce business selling a product for $100: without factoring in $10 for shipping, $5 for packaging, and a 3% merchant fee ($3), the gross margin appears higher than it truly is.

In reality, these costs reduce your actual profit per sale to $82, impacting both pricing and revenue projections.

With doola’s affordable bookkeeping, you can ensure all these expenses are accounted for, giving you a true view of profitability and helping you set realistic goals.

3. Poor Inventory Management

Managing inventory across multiple channels like Shopify and Amazon can be tricky.

Without careful tracking, businesses often face stockouts, missed sales, or excess inventory that eats into profits.

A robust inventory management system is essential to balance stock levels, avoid costly errors, and maintain healthy cash flow.

Example:

Let’s say you’re selling a popular product on both Amazon and Shopify, aiming to keep 200 units in stock.

Now let us consider two scenarios.

Scenario	Units on Hand	Units Sold on Amazon	Units Sold on Shopify	Ending Stock	Outcome
Poor Tracking	200	150	100	-50	Stockout on Amazon, overstock on Shopify, lost sales on both channels
Reliable System in Place	200	100	100	0	Balanced inventory, steady sales, and minimal carrying costs

With a reliable tracking system, you can automatically update inventory across channels as units sell, preventing stockouts and costly overstocks.

4. Misinterpreting Ecommerce Financing Options

Ecommerce financing tools, such as Shopify Capital and Stripe Capital, differ from traditional loans in their structure and repayment methods.

Instead of fixed monthly payments, these financing options typically involve automatic deductions from future sales, which can fluctuate depending on your revenue.

Misclassifying these funds as traditional loans can lead to cash flow surprises and financial mismanagement.

Example:

Suppose you receive $10,000 from Shopify Capital with a 10% repayment rate on sales. If you make $5,000 in sales one month, Shopify will deduct $500 (10%) as repayment.

In a lower-sales month, the deduction would be smaller. Without proper tracking, these automatic deductions can create unexpected cash flow gaps.

The table below provides a complete overview.

Scenario	Monthly Sales	Automatic Deduction (10%)	Remaining Cash Flow
High Sales Month	$5,000	$500	$4,500
Low Sales Month	$2,000	$200	$1,800

✅ doola Tip

To avoid surprises, record these financing repayments accurately. With doola Bookkeeping, you’ll have a clear view of cash flow, ensuring these deductions don’t catch you off guard.

Check out how doola Bookkeeping works.

5. Sales Tax Compliance Challenges

State-by-state tax obligations often make ecommerce sales tax extremely complex. Each state has its own tax rates, thresholds, and requirements.

And therefore:

Staying compliant requires tracking these variations carefully to avoid penalties.

For instance, if you’re selling to customers across the US, you may need to collect and remit different sales taxes in multiple states.

Missing these obligations or miscalculating tax liabilities can lead to hefty penalties and audits down the road.

✅ How Can doola Bookkeeping Help?

With doola’s bookkeeping services, you can seamlessly manage sales tax obligations, ensuring each transaction is properly categorized and tracked by state.

This way, you avoid the risk of non-compliance while saving valuable time — allowing you to focus on growing your ecommerce business confidently.

Book a demo and let our experts handle your compliance challenges.

6. Inadequate or Generic Chart of Accounts (CoA)

An off-the-shelf Chart of Accounts (CoA) might work for traditional businesses, but it often falls short for ecommerce.

Ecommerce businesses have unique cost structures—such as fulfillment fees, advertising spend, and transaction costs — that require tailored categories to accurately track spending and assess profitability.

Without this customization, you risk missing critical details that could impact your decision-making and profitability.

How Do I Optimize My Chart of Accounts?

To optimize your CoA, include specific categories that reflect your ecommerce expenses:

✔️ Marketing and Advertising Expenses:

Instead of lumping all marketing costs together, break them down by campaign or channel, such as “Facebook Ads,” “Influencer Collaborations,” or “Email Marketing.”

This provides a clearer view of which channels drive the best return on investment (ROI), allowing you to allocate resources more strategically.

✔️ Cost of Goods Sold (COGS):

For a more accurate profit margin, itemize COGS into categories like:

For example:

Separating “Inbound Freight” (the cost to bring products into your warehouse) from “Outbound Freight” (shipping to customers) helps you understand your total product cost and set prices accordingly.

✅ How Can doola Bookkeeping Help?

With doola’s cost-effective bookkeeping support, you can customize your CoA to capture these essential categories, giving you granular insights into each area of your business.

This level of detail empowers you to make better financial decisions, optimize spending, and maximize your profitability.

7. Neglecting Cash Flow Tracking for Accurate Financial Statements

While accrual accounting is essential for ecommerce, neglecting cash flow tracking can lead to major blind spots.

In accrual accounting, you record revenue when a sale is made, not when cash is received — which means your financial statements might show profit on paper, even if cash isn’t available.

For ecommerce, where refunds, payment delays, and vendor payments are common, this can lead to inaccurate forecasts and cash flow surprises.

Example:

Let’s say an ecommerce business records a $1,000 sale in December, expecting the funds to be available immediately.

However, due to payment processor delays, only $800 is received in December, with the remaining $200 arriving in January, after deducting processing fees.

Additionally, a customer requests a $50 refund, impacting the actual cash received.

Here’s a breakdown of how this impacts cash flow:

Transaction	Expected Amount	Actual Cash Received	Notes
Sale in December	$1,000	$800 (initial payment)	Payment delayed, fees deducted
Remaining Payment in January	$200	$200	Received after deduction
Refund Requested	N/A	-$50	Refund processed
Total Cash Received	$1,000	$950	Reduced due to fees & refund

In this case, the business’s profit looks like $1,000 on paper for December, but only $950 is available as cash.

Without tracking these discrepancies, the business may overestimate available funds and face cash flow shortages.

✅ How Can doola Bookkeeping Help?

With doola Bookkeeping, you can monitor cash flow closely alongside accrual accounting, providing a complete financial picture.

It helps ensure accurate cash flow statements, so you always know how much cash you actually have on hand, enabling better planning and avoiding unexpected shortfalls.

Financial Statements You Need for Ecommerce Bookkeeping

To run a successful ecommerce business, you need a solid set of financial statements to guide decision-making and track performance.

Here are the three key financial reports every ecommerce owner needs:

1. Income Statement:

This report details your revenue, expenses, and net profit, highlighting which products or campaigns generate the most profit. Use it to identify and prioritize high-performing areas in your business.

2. Balance Sheet:

Provides a snapshot of your assets, liabilities, and equity, helping you understand the financial health of your business.

3. Cash Flow Statement:

By tracking cash inflows and outflows, this report is vital for managing cash flow and ensuring liquidity.

It gives you a clear view of your available cash to cover operational expenses and navigate financial obligations.

With all the above statements, you gain a comprehensive view of your business’s financial situation, allowing you to make proactive, strategic choices for growth.

Top 3 Ecommerce Bookkeeping Software Tools

Ecommerce bookkeeping comes with unique demands, but the right software can simplify the process.

Here are 3 top tools built for ecommerce businesses:

doola Bookkeeping

Tailored for ecommerce, doola Bookkeeping streamlines financial management by offering:

• Integration with leading ecommerce platforms

• Automation of sales tax compliance

• Intuitive tracking and monitoring

It’s ideal for DTC brands looking to focus more on growth and less on complex bookkeeping.

QuickBooks Online

Known for its versatility, QuickBooks offers robust inventory tracking, detailed expense management, and seamless integrations with most ecommerce platforms.

Ideal for mid-sized businesses, it provides comprehensive reporting to help you stay on top of financial insights.

Xero

With a user-friendly interface and robust reporting features, Xero is popular among small to mid-sized ecommerce businesses.

Its capabilities include easy bank reconciliation, customizable invoicing, and sales tax tracking, making financial tracking straightforward.

Each tool caters to different business sizes and accounting needs, so choose the one that best matches your sales channels and scale to keep your bookkeeping accurate and efficient.

Important Ecommerce Bookkeeping Features

When choosing or optimizing your ecommerce bookkeeping system, focus on these essential features to meet the unique demands of online businesses:

✔️ Multi-Channel Integration:

Seamlessly connect with all your sales platforms — Shopify, Amazon, eBay, and more — for unified, consolidated reporting.

✔️ Sales Tax Management:

Simplify compliance with automated sales tax tracking across states, ensuring you stay on top of ever-changing regulations.

✔️ Automated Reconciliation:

Minimize errors with automated reconciliation of merchant fees, inventory costs, and returns, streamlining your bookkeeping process.

✔️ Inventory Tracking:

Monitor stock levels and values across all channels in real time to avoid overselling or stockouts.

✔️ Real-Time Financial Reporting:

Access to real-time data gives you a clear view of performance, cash flow, and profitability at any given point.

Optimizing your bookkeeping system with these features ensures smoother operations and sets your ecommerce business up for scalable success.

Discover doola Bookkeeping — Your Partner in Ecommerce Success

Ecommerce bookkeeping can be complex, but with doola, you don’t have to face it alone.

We specialize in helping ecommerce and DTC businesses navigate these challenges with expert bookkeeping services tailored to the unique needs of online retail.

With doola by your side, you’ll get more than just data entry — we offer insights to help you optimize profitability and stay on top of compliance.

Book a free demo today and let us help you take your ecommerce business to new heights!