The Hidden Costs of Running an Online Store (And How to Plan for Them)
Published
26 May, 2025
4 min read
Starting an online store can feel like a dream come true. Low overhead, the ability to work from anywhere, and access to a global customer base — what’s not to love? But here’s what most eCommerce guides won’t tell you: there are hidden costs lurking behind those tempting profit projections.
If you don’t plan for them upfront, these expenses can eat away at your margins and derail your business before it finds its footing. Let’s unpack what these hidden costs are and how you can stay ahead of them.
Sure, online payment gateways like PayPal, Stripe, and Shopify Payments make it easy to get paid. But convenience comes at a cost. Most processors take a cut of every sale — typically 2.9% + $0.30 per transaction in the U.S.
Why it matters:
When your average order value is low, these fees stack up fast. If you don’t factor them into your pricing, you’re giving away a slice of your profit on every sale..
How to plan for it:
Include processing fees in your pricing strategy. If your platform offers multiple payment options, compare rates and choose what makes financial sense for your volume.
Customers expect easy, hassle-free returns. And while offering them boosts trust and conversion rates, it can also become a costly headache. Beyond losing the sale, you’ll often eat the shipping costs, restocking fees, and in some cases, the product itself if it’s unsellable.
Why it matters:
Unexpected spikes in returns can drain your cash flow. Chargebacks, where customers dispute a charge with their bank, often carry additional fees and can even threaten your merchant account if excessive.
How to plan for it:
Establish a clear, fair return policy and communicate it upfront. Budget a percentage of your revenue (usually 1-5%) to cover refunds and chargebacks.
Free shipping may win customers, but it isn’t free for you. Beyond postage, you’ll need to factor in packaging materials, labels, handling, and storage if you're using third-party fulfillment services like ShipBob or Amazon FBA.
Why it matters:
If you’re not calculating the full cost of getting a product to a customer’s doorstep, you risk selling at a loss.
How to plan for it:
Use shipping calculators to get accurate rates. Build shipping fees into your pricing or offer it conditionally (e.g., free shipping over $75). Regularly review your options to keep costs competitive.
Your website isn’t a one-time expense. There are ongoing costs for hosting, SSL certificates, software updates, and technical support. Premium themes, plugins, and third-party tools for SEO, analytics, or email marketing can quickly add up.
Why it matters:
A neglected site is a security risk and a conversion killer. Slow, glitchy stores cost sales.
How to plan for it:
Budget a fixed monthly or annual amount for web maintenance. Audit your tools regularly and cancel underused services.
Launching a site doesn’t mean customers will magically appear. Paid ads on Google, Facebook, Instagram, or TikTok are almost unavoidable if you want to drive traffic. Costs can fluctuate wildly based on competition and targeting.
Why it matters:
Many new eCommerce owners underestimate how much they’ll need to spend to acquire customers, especially early on.
How to plan for it:
Start with a modest ad budget, then scale based on ROI. Balance paid ads with organic strategies like SEO, social media, and content marketing to diversify your traffic sources.
Running an online store often requires a suite of tools: email marketing platforms, customer support apps, inventory management software, design programs, and analytics services. While many start free or cheap, monthly fees stack up over time.
Why it matters:
Recurring software subscriptions can silently siphon profits, especially if you aren’t tracking what you’re actually using.
How to plan for it:
Create a software budget and audit your subscriptions quarterly. Look for tools that offer multiple features to consolidate expenses.
Online sales tax laws are a moving target, with rules varying by state and country. You’ll need to track and collect the right tax rates and possibly file in multiple jurisdictions. Add accounting software or professional services to the mix, and it’s another recurring cost.
Why it matters:
Non-compliance can mean fines, back taxes, and legal trouble.
How to plan for it:
Invest in reliable tax software or consult with an eCommerce-savvy accountant early. Set aside funds regularly for tax obligations — don’t treat it as leftover money.
The real cost of running an online store isn’t just your inventory and website setup. It’s the dozens of small, recurring expenses that can quietly chip away at your profits if you’re not paying attention.
The key is awareness and planning. Map out every potential cost category before you launch, keep a running budget, and review it monthly. That way, you’re not caught off guard, and your eCommerce business can grow on solid, sustainable ground.
Pro tip:
Consider building a simple cost-tracking spreadsheet or using accounting tools like QuickBooks or Xero specifically tailored for small online businesses.
