The number of ecommerce platforms and apps available now means starting an online store is incredibly accessible. Keeping one alive is another matter.
Global ecommerce sales are projected to reach $7.89 trillion in 2028. But behind that headline sits a harder reality.
Google Shopping cost per clicks (CPCs) jumped 33.72% in 2025. Every $1 of fraud now costs US ecommerce businesses an average of $4.61. Seven in 10 shoppers abandon their carts before checkout. And only 7% of online retailers have achieved true unified commerce across their channels.
Some of these challenges affect nearly every business. This guide breaks down the biggest ecommerce challenges store owners face in 2026 and how to address them.
What are the most common ecommerce challenges?
The challenges facing your business will evolve over time. As customer expectations shift and your operations become more complex, you’ll solve some problems and encounter new ones.
Challenges for new store owners
The first challenge for a new store is being found. With paid acquisition costs rising and organic search taking time to build, getting quality traffic to an unknown brand is hard. When visitors do arrive, converting them is harder still.
New stores have no reviews, no brand recognition, and no established trust, and according to the Baymard Institute, 19% of shoppers abandon checkout specifically because they don’t trust the site with their payment information.
If you’re a new store owner, you might find yourself up against these challenges:
- Standing out in a crowded market
- Driving quality traffic to your store
- Converting visitors into buyers and generating customer engagement
- Payment processing and checkout trust
- Data privacy and customer trust
- Cart abandonment and checkout friction
Challenges for growing businesses
Growth brings a whole new set of problems. As stores expand across channels, businesses often struggle to keep inventory, fulfillment, customer data, and operations aligned.
If you’re an established store owner looking to grow, look out for these challenges:
- Building repeat purchase habits
- Rising customer expectations
- Personalizing the shopping experience
- Managing inventory and order fulfillment
- Choosing the right tools with overcomplicating your stack
- Scaling without breaking your operations
- Cybersecurity threats and fraud prevention
- Building an omnichannel experience
- Expanding into international markets
- Staying competitive on marketplaces
Getting customers: traffic, acquisition, and visibility
Here are the core challenges around attracting and converting customers.
Standing out in a crowded market
According to research by Retail Economics, 27% of retailers say navigating the growing online competition is one of their biggest challenges at the moment. It makes sense. There are 25.1 million online stores worldwide, a figure that more than doubled during the pandemic and has kept climbing, with an average of 2,740 new stores launching every day.
In short: There’s a lot of competition and shoppers can be fickle. VML’s Future Shopper 2025 report found that 45% of global shoppers regularly abandon purchases because the customer experience on offer is too frustrating.
Retailers must compete not only for attention, but also for customer trust and loyalty.
What to do:
- Define a specific customer persona. Who your store is for matters more than what it sells. “We are very in touch with our community and what they’re into. If we take that and apply it to our ecom, we’ve seen a lot of great results,” says Jeff Eiser, co-founder of Revenge Of, a comic book shop in Los Angeles, in an interview with Shopify Masters.
- Audit your competitors’ messaging and find the angle they’re missing.
Driving quality traffic to your store
Semrush’s 2025 traffic channel analysis, which examined billions of web visits, found organic search accounts for 16% of total traffic, which is more than 32 times the share driven by paid search. This has pushed store owners toward owned and earned channels, as well as marketing strategies like search engine optimization (SEO), email, social, and referral.
But there’s another, newer search layer in the mix. Capgemini’s 2025 consumer research found that 58% of consumers have replaced traditional search engines with generative AI tools for recommendations. This means brands are having to juggle traditional search optimization techniques with those that also work for AI-powered search.
What to do:
- Build an SEO strategy around transactional and comparison keywords as well as brand terms.
- Optimize your store for AI recommendation engines and search assistants.
- Use email as an acquisition channel. Capture subscribers through pop-ups, lead magnets, and post-purchase flows before they leave your store.
- Audit your paid spend. Cut campaigns with return on ad spend (ROAS) below your break-even and reinvest in creative testing for channels where performance is improving.
Converting visitors into buyers
IRP Commerce, which publishes monthly conversion benchmarks from live business transaction data, put the all-industry average ecommerce conversion rate at 1.7% in April 2026, which is lower than the previous year. That means fewer than two in every 100 visitors buy.
Contentsquare’s 2025 Digital Experience Benchmarks report, which analyzed 29 billion visits across 2,276 retail sites, found overall conversion rates dropped 5.5% year on year. New visitors were hit hardest, with their conversion rate falling 8.9%, compared to a 4% drop for returning visitors.
The gap is widest in categories where shoppers tend to mull over their decision for longer. For example, luxury categories convert at 1.4% on desktop and just 0.9% for mobile commerce, while Health & Beauty’s mobile conversion rate reaches 3.4%.
Visits are shorter and fewer are converting, which means the window to turn intent into a sale is shrinking.
What to do:
- Run your store through Google PageSpeed Insights to find out how quickly it loads and where you can make improvements.
- Write product descriptions that answer the real questions your customer has before buying, including information about sizing, materials, use cases, and what makes this product different from the cheaper alternative.
- Enable Shop Pay. An independent study by a Big Three management consulting firm found it lifts conversion by up to 50% compared to guest checkout, and outpaces other accelerated checkouts by at least 10%.
Keeping customers: retention, engagement, and loyalty
Acquiring a customer is just the beginning. You then need to get them to come back. These are some of the biggest retentional challenges in ecommerce.
Cart abandonment and checkout friction
The Baymard Institute tracks shopping cart abandonment across 50 studies and puts the 2026 average at 70.22%. That figure climbs to 85.65% on mobile devices.
That means for every 10 shoppers who add something to their cart, seven or more leave before buying.
The top reasons, according to Baymard, are due to shoppers not yet being ready to buy (43%), extra costs at checkout (39%), and the delivery being too slow (21%).
“Our early days of ecommerce, we did actually lose money. I remember thinking, ‘Can we just ban ecommerce and do more stores? Is it too hard? Is it too much work?’” says Simon Beard, co-founder of Culture Kings.
Culture Kings eventually moved to Shopify Plus and overhauled its checkout. Simon describes the turnaround: “I really felt like the floodgates opened,” says Simon. “We had the stability. Anything I wanted to do, it seemed possible.”
What to do:
- Don’t make shoppers create an account to buy. Always offer guest checkout as the primary path. Shopify’s one-page checkout reduces the average checkout to less than two minutes.
- Be transparent about shipping costs from the product page as well as at checkout. Unexpected fees are one of the biggest abandonment triggers.
- Set up an abandoned cart flow. Klaviyo’s 2026 benchmarks found that automated email flows generate revenue per recipient nearly 18 times higher than email campaigns on average, with top-performing flows reaching $7.79 per recipient.
Building repeat purchase habits
A separate Klaviyo study reports that 73% of B2C marketers say that customer acquisition costs are rising. In fact, 28% of retailers claim that tackling high customer acquisition costs is one of the main challenges facing them this year.
A one-time buyer becomes an expensive loss when acquisition costs keep climbing. The only way to make the economics work is to bring existing customers back.
What to do:
- Launch a post-purchase email sequence covering order confirmation, shipping updates, and a follow-up several days after delivery with related products. Shopify Messaging handles this from your admin without needing a third-party tool.
- Introduce a customer loyalty program. Smile.io’s State of Customer Loyalty in Ecommerce report, which analyzed 585 million orders across 100,000 merchants, found loyalty-generated value grew year-on-year across every major ecommerce industry, with brands processing 500 to 5,000 monthly orders seeing the largest gains at 23.93% year over year growth.
- Track repeat customer rate in Shopify Analytics.
Personalizing the shopping experience
According to Klaviyo’s 2025 Future of Consumer Marketing report, 74% of shoppers expect more personalized experiences from brands. Yet 34% can’t remember a brand personalizing an experience for them in the previous six months.
You don’t need a sophisticated tech stack to make personalization work. Start with customer data you already have, including purchase history and browsing behavior, both of which tell you what customers are interested in and when they’re most likely to buy again.
What to do:
- Segment your email list by customer behavior and use that data to send highly relevant product recommendations and content.
- Add a product recommendation section to your homepage and product pages. Shopify’s native recommendation engine surfaces related and frequently bought-together products automatically.
- Use browse and purchase data to personalize your on-site search results and featured collections.
Running the business: operations, fulfillment, and tech
The processes running your online business determine how well you can manage the day-to-day logistics and supply chain. Here are some of the most common operational challenges.
Managing inventory and order fulfillment
Stockouts cost global retailers $1.2 trillion annually, and 29% of customers will walk away from carts if a product is out-of-stock.
This isn’t really a surprise, but a large number of retailers don’t actually know what they have in stock.
Only 36% of retailers say they have full inventory visibility, while 57% report gaps across channels, according to Linnworks’ State of Commerce Ops 2025 report.
Paul & Joe, the Japanese cosmetics brand, launched its online store specifically to reach customers who couldn’t access their limited physical locations.
“One of the reasons for launching the online store was the limited number of physical stores,” says Takayuki Sakakibara, group leader at Paul & Joe. “There were customers interested in the brand but couldn’t purchase products because there were no stores nearby.” Its ecommerce channel grew by 400% after moving to Shopify Plus and gaining real-time inventory visibility across markets.
What to do:
- Set reorder points for every SKU. Know your average days of supply for each product and set alerts at the point where you can still restock before running out.
- Use inventory management software to centralize everything. Shopify’s inventory tools sync stock in real time across your online store, Shopify POS, and any connected sales channels.
- Build supplier lead times into your forecasting. If your supplier takes three weeks to ship, your reorder point should account for that plus a buffer for any spikes in demand.
Choosing the right tools without overcomplicating your tech stack
The research from Retail Economics also found that 33% of North American retailers say adopting AI and emerging technologies is their main performance challenge in 2026.
Gartner’s 2025 Marketing Technology Survey found that marketers actively use just 49% of their technology stack’s capabilities, even as marketing technology accounts for 22% of total marketing spend. Only 15% of organizations are considered top performers, which means their tools actually meet strategic goals and deliver measurable return on investment (ROI). The rest suggests many organizations are paying for capability they’re not using.
For ecommerce store owners the cost is so much higher than just financial. Every disconnected tool creates a data gap. For example, you might process orders in one tool that doesn’t update inventory in another.
What to do:
- Audit your current stack. For each tool, ask: Does it solve a problem I can’t solve with a built-in Shopify feature? Start with Shopify’s native capabilities. Analytics, email, shipping, and multiple payment options are all available without third-party apps.
- When you do need a third-party app, use the Shopify App Store and filter by “Built for Shopify” status. These apps meet higher standards for performance and Shopify integration, and have been tested against the platform’s APIs.
Scaling without breaking your operations
Linnworks’ State of Commerce Ops 2025 report further reports that 86% of retailers said they’d had a jump in revenue or order volume in 2024. More than a third saw order volumes jump more than 20%, and nearly half grew between 5% and 20%. But it wasn’t all plain sailing. Brands struggled to keep up with the surge of new orders, hence the large number of retailers who had limited visibility into their inventory.
What to do:
- Automate high-volume, easy tasks first. Shopify Flow lets you build automations for inventory alerts, fraud review, order tagging, and customer segmentation without code.
- Use Shopify Sidekick, Shopify’s built-in AI assistant, to speed up product description writing, analyze store performance, and get guidance on specific tasks.
- Build your fulfillment operation to handle your peak volume. Your packing process and carrier agreements need to be able to support your busiest week.
Protecting your business: security, data, and payments
The bigger your store gets, the more attractive a target it becomes, and the more costly the consequences when something goes wrong. Here are the key security challenges store owners face today.
Cybersecurity threats and fraud prevention
Fraud affects more than the bottom line. The 2025 LexisNexis True Cost of Fraud Study study also found that 64% of respondents said fraud hurts customer conversion rates, while 63% reported increased customer churn as a result of fraud.
Chargeback penalties, processing fees, manual review time, and lost customers all pile on top the original cost loss. There’s also a cost on the other side. The same study found that 36% to 37% of US customers abandon a transaction when fraud checks feel too intrusive.
Every fraudulent transaction costs store owners more than four times the original loss once chargebacks, fees, and review time are added up.
What to do:
- Use Shopify Payments for built-in PCI compliance, SSL, and fraud detection. It includes chargeback management and automatically flags high-risk orders for review, without requiring a third-party fraud tool.
- Review Shopify’s built-in fraud analysis on every order flagged as high-risk. Look for mismatches between billing and shipping addresses, unusual order values, and multiple failed payment attempts.
- Set clear, written return and refund policies and automate enforcement.
Payment processing and checkout trust
Nineteen percent of shoppers abandon checkout because they don’t trust the site with their payment information.
For new stores, this is a genuine challenge. Without brand recognition, you have to earn trust at the exact moment a shopper is most hesitant.
What to do:
- Display security badges near your payment fields. Shopify Payments includes fraud detection, automatic SSL, and card verification built into the standard setup.
- Offer the payment methods your customers actually use. Twenty-six percent of US shoppers are more likely to buy when a buy now, pay later (BNPL) option is offered.
- Be transparent about transaction fees. Third-party payment provider fees are unavoidable costs that your pricing needs to absorb.
Data privacy and customer trust
Cisco’s Consumer Privacy Survey, an annual global study of consumer attitudes toward data privacy and data security, found that more than 75% of consumers won’t buy from a company they don’t trust with their data.
If shoppers can’t verify how their customer data will be used, they just won’t buy, no matter how good the product or price. Privacy regulations like General Data Protection Regulation (GDPR) and California Consumer Privacy Act (CCPA) also add a compliance layer on top of this, with requirements that vary by market and carry penalties for getting wrong. And, if you’re selling internationally, those requirements multiply every time you enter a new market.
What to do:
- Write a clear, plain-language privacy policy. Link it from your footer, your checkout, and anywhere you collect customer data.
- Only collect data you actually use.
- Use Shopify’s built-in cookie consent and data export tools to handle GDPR and CCPA compliance requests without custom development.
Selling across channels and borders
Reaching customers beyond your own store opens up real opportunity, as well as new challenges for every channel and market you add.
Building an omnichannel experience
VML’s Future Shopper 2025 report, which surveyed more than 25,000 shoppers across 16 countries, found that 62% of global shoppers prefer buying from brands that have both a physical store and an online presence. Shoppers aren’t choosing between channels—they’re moving between them freely and expecting the experience to hold together at every step.
Most retailers aren’t keeping up. Manhattan Associates’ 2026 Global Unified Commerce Benchmark found only 7% have achieved true unified commerce leadership. A third are still in the “basic” category.
What to do:
- Unify your inventory across channels. Shops using Shopify POS alongside their online store to unify inventory, transactions, and customer data have reported overall growth in both retail POS and online sales.
- Maintain consistent pricing, promotions, and product information across every channel to keep customer satisfaction high.
Expanding into international markets
Cross-border ecommerce accounted for approximately 18.8% of all global online sales in 2025, with 59% of global shoppers buying from retailers outside their home country.
DHL’s 2025 Cross-Border Buying Behavior Trends report found that fear of fraud is the leading reason shoppers hesitate to buy from international retailers (52%). Delivery expectations create additional friction, with DHL reporting that poor delivery and returns experiences can lead up to four in five shoppers to abandon their carts.
What to do:
- Use Shopify Markets to sell internationally from a single Shopify store. It handles localised pricing, currency conversion, duty and tax calculation, and market-specific domains without requiring separate store instances.
- Test one or two international markets before building a full global infrastructure. Look at where your traffic is already coming from.
- Localize more than just currency. Research what shoppers in the markets you want to expand into expect in terms of payment methods, returns, and delivery times.
Staying competitive on marketplaces
ChannelEngine’s Marketplace Shopping Behavior Report 2025 found that 37% of consumers now begin product searches on marketplaces. Shoppers also compare products across an average of three marketplaces before purchasing, highlighting how competitive marketplace environments have become.
ChannelEngine’s Marketplace Seller Trends Report 2025, which surveyed 470 sellers across the US and Europe, found the average seller is now active on no less than six marketplaces, with more than a third active on seven or more.
Yes, marketplaces put your products in front of potential customers who are already searching, but they also put your competitors’ products there too. Managing listings, pricing, and inventory across six or more platforms all at once is no easy feat and it only compounds as you add channels.
What to do:
- Connect your Shopify store to Amazon, eBay, and other sales channels through Shopify Marketplace Connect. You can manage listings and inventory from one place without manually duplicating work across platforms.
- Differentiate on marketplaces with bundles, kits, or configurations not available from mass-market competitors.
- Use marketplace sales to build your email list. Every buyer who purchased on a marketplace is a potential direct customer. You could include a card in your packaging that gives them a reason to visit your store directly.
Ecommerce challenges FAQ
What are the biggest challenges in ecommerce right now?
Rising acquisition costs, cart abandonment, and fraud. Google Shopping CPCs jumped 33.72% in 2025, seven in 10 shoppers abandon their carts before buying, and US businesses now lose $4.61 for every $1 of fraud.
What are the main challenges of starting an ecommerce business?
Getting found is the first hurdle, followed by converting visitors who don’t yet know or trust your brand. Early-stage stores can also struggle with everything involved in running the business day-to-day, including fulfilling orders reliably, handling returns, and responding to customers.
How do you overcome ecommerce challenges?
Most challenges have a predictable root cause and respond well to fixing the right thing rather than everything at once. The stores that improve fastest tend to identify their biggest single leak, fix it with data rather than instinct, and build from there.
What are the challenges of ecommerce compared to physical retail?
Physical retail lets customers interact with products in the moment, buy instantly, and get any questions answered by a real human being who’s right there in the store. Ecommerce compensates with photography, copy, reviews, and fast delivery promises, but also carries return rates of 19.3% compared to around 10% in-store, and has to work harder to build the trust that a physical presence provides as standard.
How does Shopify help with common ecommerce challenges?
Shopify addresses most challenges with built-in tools rather than requiring a separate product for each one. Shop Pay lifts checkout conversion by up to 50% compared to guest checkout. Shopify Payments handles PCI compliance and fraud detection. Shopify Shipping provides discounted carrier rates. Shopify Markets enables international selling. Shopify POS unifies online and in-person selling. The platform’s value is that store owners can address most standard challenges without assembling a separate tool stack.
