12 Top Ecommerce Challenges and How to Master Them

Selling online has never been easier. Running a successful ecommerce operation? That’s a different story. While digital platforms have made it possible for brands of all sizes to reach customers directly, that access comes with rising operational demands. Competition is fierce, margins are tight, and customer expectations related to speed, service, and experience keep climbing. Meanwhile, certain challenges show up again and again—audience targeting, channel overload, fulfillment delays, budget misfires, and tech stack sprawl, to name a few. But with the right strategies and tools in place, it’s possible to cut through the chaos, meet customer needs, and build a business that scales.

What Is Ecommerce?

Ecommerce, short for electronic commerce, is the act of buying and selling goods or services online. It includes everything from consumers ordering products through retail websites or marketplaces to B2B distributors managing recurring orders through online portals. Whether it takes place through desktop sites, mobile apps, or integrated platforms, ecommerce has become a foundational part of modern commerce—not just a backup plan for brick-and-mortar stores, but an end-to-end business model that demands just as much coordination as a physical storefront, if not more.

Key Takeaways

• Ecommerce businesses face pressure to reach the right audiences and convert prospects effectively in a crowded market.
• Marketing is often one of the largest ongoing expenses in ecommerce, but overspending on the wrong channels can limit ROI.
• Gaps between customer-facing and back-end operations can cause delays, confusion, and slower growth.
• Connecting ecommerce data with inventory, financials, and customer information lays the groundwork for automated operations that reduce busywork.

Ecommerce Challenges Explained

Running an ecommerce business can feel like trying to hit a moving target. Just when you’ve nailed the right marketing channel or fulfillment rhythm, a new algorithm update, competitor, or shift in customer expectations throws everything off balance. Ecommerce today moves faster and feels more competitive than ever. For ecommerce brands trying to grow or simply stay steady, the hard part isn’t launching an online store; it’s optimizing every part of the operation so that it works together. That means aligning sales, inventory, fulfillment, customer support, and marketing—and being ready to adapt when demand changes.

The complexity grows when these issues stack and overlap. Rising shipping costs don’t just shrink margins; they influence return policies, impair checkout, and make it harder to retain customers. Poor website performance can derail marketing campaigns, hurt conversions, and drive cart abandonment. Other core challenges—siloed data, fragmented technology stacks, inconsistent customer experiences, inefficient returns—aren’t new. But they add up, creating friction that can’t be ignored.

Shoppers expect more, and they want it faster. Seamless, reliable experiences aren’t a nice-to-have; they’re the baseline. To meet that bar, ecommerce businesses need more than a basic online storefront. They need a thoughtful, tightly coordinated approach to decision-making across every layer of the business.

How to Overcome the Top 12 Common Ecommerce Challenges

Knowing how to sell online is one small piece of the ecommerce puzzle. The real challenge lies in solving everything that comes with it. From reaching the right audience to keeping up with competitors to converting visitors once they land, each additional puzzle piece comes with its own set of brainteasers. Here are 12 of the most common challenges ecommerce businesses face—and ways to tackle them that actually move the needle.

1. Reaching the Right Users

   You can have the best product on the market, but if it’s not getting in front of the right people, it won’t sell. For many ecommerce businesses, the challenge isn’t attracting traffic—it’s attracting qualified traffic. Casting too wide a net wastes ad spend and floods your site with visitors who bounce without converting. That kind of misalignment can also skew your analytics, making it harder to see what’s actually working.

   To remedy this, begin by refining your targeting. Use first-party data (drawn from past purchases or onsite behavior) and segment audiences according to how they shop or interact with your brand. Social platforms, for example, allow for highly tailored campaigns based on demographics, interests, and shopping preferences—making it easier to reach the right audience. It’s also worth building out detailed buyer personas and auditing your top-performing traffic sources to see which ones align best with your ideal customer base.

2. Converting More Visitors Into Customers

   Attracting potential buyers is only half the equation; converting them is where the real work begins. Friction points, such as slow load times, confusing navigation, weak product descriptions, or missing trust signals (including reviews or security badges), can easily derail a purchase. A site that’s visually polished but functionally clunky leaves money on the table.

   Start by optimizing your product pages for clarity, speed, and usability. Include strong calls to action, high-quality images, real-time inventory indicators, and clear shipping policies. Conduct A/B tests highlighting key elements, such as headlines, button placement, and checkout flow, to identify what’s working and what isn’t. If visitors drop off at the cart stage, consider adding guest checkout options, simplifying forms, or launching retargeting campaigns to bring them back.

3. Increased Ecommerce Competition

   The digital shelf is more crowded than ever, and big-name brands aren’t the only ones delivering the pressure. Niche sellers, global marketplaces, and brands that launch and grow primarily through social media are all fighting for the same screen space—and often the same customers. For many businesses, this leads to thinner margins, higher acquisition costs, and weaker brand loyalty.

   One way to stand out is by leaning into what makes your business different. Whether that’s exceptional service, personalized experiences, ethical sourcing, or faster fulfillment, differentiation helps you define your business and gives customers a reason to come back. Investing in brand storytelling across channels can also help cut through the noise.

   Behind the scenes, consider automating operational tasks, such as inventory updates, order processing, and customer communications. Doing so can free up time and resources to focus on strategic growth.

4. Choosing the Right Marketing Channels

   Too many ecommerce marketing teams fall into the trap of trying to be everywhere at once—Instagram, Google Ads, email, TikTok, YouTube, affiliate programs. With so many marketing platforms available today, it’s easy to feel overwhelmed. And, without a clear understanding of which channels are actually bringing in qualified traffic, the upshot is often a scattered approach that burns budgets without delivering results. Worse, it gets harder to gauge what’s working and what isn’t.

   Instead of jumping onto every new platform, take a step back and assess where your best customers are coming from now and build from there. Review past campaign performance by channel, test new ones methodically (beginning with clear goals and controlled variables), and use attribution tools to track what’s driving conversions. For some businesses, that might be leaning into organic search or email. For others, paid social ads or influencer partnerships may yield better results. Either way, focusing on just two or three high-performing channels—before expanding—could lead to more consistent, efficient growth.

5. Providing a Satisfying Customer Experience

   Brick-and-mortar stores can create loyalty with in-person service and ambiance. Ecommerce doesn’t have that advantage. Everything rides on the online experience. Fast shipping, intuitive navigation, real-time updates—customers expect it all. When any of those expectations falls short, frustration builds, and it doesn’t take much for a customer to bounce or turn to a competitor. If shoppers can’t find what they’re looking for, don’t trust your return policy, or hit an error at checkout, there’s a good chance they won’t come back. Worse, a single bad experience can ripple through reviews and referrals.

   Improving customer experience isn’t about flashy design. Start by reducing friction: Trim down navigation menus, clarify product details, and ensure that key pages load quickly. Then, layer in proactive communication (such as order updates or delay alerts), flexible policies (think: easy returns or extended support hours), and a feedback loop that leads to real improvement—whether that means adjusting product pages or fixing common service issues. Investing in customer experience is about earning trust and keeping people coming back over the long run. Small, targeted improvements can reap big rewards when they’re rooted in resolving actual pain points.

6. Maintaining Strong Security and Privacy Controls

   Ecommerce businesses handle sensitive customer data every day, from payment details to personal information. A single breach or misstep can tank customer trust, trigger legal consequences, or jeopardize your entire operation. And in light of ever-evolving privacy laws, “good enough” security doesn’t cut it.

   Begin with the basics: secure hosting, HTTPS, and strong, regularly updated passwords. Then go further. Use PCI-compliant platforms that meet industry standards for handling payment data, restrict access to sensitive information, and make your privacy policy easy to find and understand. Be clear about what customer data you collect, why you collect it, and who has access to it.

   Most importantly, don’t wait until there’s a problem. Data security should be built into your operations from day one. Make it part of your daily operations through routine software updates, employee access reviews, and built-in encryption for customer data.

7. Managing Returns and Refunds

   In brick-and-mortar stores, returns happen on the spot. In ecommerce, they involve packaging, logistics, and restocking—creating added strain on your operations. If the return process is slow, unclear, or inconvenient, it chips away at customer trust and, ultimately, your bottom line. Between rising logistics costs and the risk of refund abuse, a poor return process can drain time, money, and goodwill.

   One way to get ahead of it is by making your return policy easy to find and simple to follow. Use plain language, set clear time frames, and communicate exactly how the process works. Automate what you can—return labels, confirmations, restocking workflows—so your team isn’t stuck chasing paper trails. And if certain products see high return rates, flag those SKUs for deeper analysis. It could be a sizing issue, a quality concern, or a mismatch with buyer expectations.

8. Fulfilling Sales Across Borders

   Selling internationally can unlock massive growth, but, when it concerns physical goods, cross-border ecommerce fulfillment brings its own set of headaches: customs regulations, tax compliance, higher shipping costs, and potential delays. Mismanaging any one of those areas—through unclear fees, customs hiccups, or uncommunicated delays—can frustrate customers or turn a first-time buyer into a one-time buyer.

   The key is to plan ahead. Before expanding into new markets, research which countries make the most sense to target and thoroughly look into their import requirements. Partner with shippers that have experience handling customs documentation in those regions, and be up front with customers about when items will arrive and whether additional fees apply. Use local language on your website and in customer communications to make the experience feel native to international buyers. And, if possible, offer local payment methods to show buyers you are actually prepared to serve them.

9. Balancing the Marketing Budget

   Marketing is one of the biggest challenges—and one of the largest ongoing expenses—in ecommerce. Without tight tracking, it’s easy to overspend on low-impact channels or underinvest in campaigns that actually perform. If margins are already thin, budget misallocation can slow growth and limit flexibility.

   Track performance closely, but don’t get lost in vanity metrics like clicks and impressions. Instead, focus on data that directly reflects what’s driving revenue, such as conversion rate, customer lifetime value, and return on ad spend. Test often by running A/B experiments on creative approaches, audiences, or messaging, and reallocate your budget based on real results. If a channel underperforms, reduce spend and prioritize what’s working. If you’re working with a small team or constrained marketing budget, prioritize campaigns with a clear path to ROI before investing in broader brand awareness. Abandoned-cart emails, retargeting, or referral programs are all good places to begin.

   

10. Handling Logistics and Supply Chain

    A smooth ecommerce experience depends on reliable fulfillment. When it falls short because of delays, back orders, miscommunications, or supplier bottlenecks, the entire operation can feel broken—no matter how polished the front end is. Unlike physical stores, where inventory and service are handled onsite, ecommerce relies on real-time coordination across tools and teams that may not even be in the same country. When systems don’t sync, or you’re still relying on spreadsheets to track inventory, the cracks can start to show.

    A solid foundation starts with real-time data, accurate forecasting, and seamlessly integrated systems. That’s where supply chain management (SCM) software comes in. It centralizes logistics operations, aligns inventory with demand, improves coordination with suppliers, and makes it easier to respond when disruptions—such as delayed shipments or sudden surges in demand—hit. The more scalable and responsive your logistics, the easier it will be to grow without burning out your team or budget.

11. Meeting Customer Delivery Expectations

    Two-day shipping used to be a perk. Now, it’s the baseline. Unlike in-store shoppers who walk out with their purchases, ecommerce customers are entirely at the mercy of delivery—making fast shipping, clear options, and real-time tracking essential. If customer expectations aren’t met, the result is often cart abandonment, customer complaints, or lost loyalty.

    You don’t have to promise same-day delivery, but you do need to set expectations early. Be forthcoming about timelines, clearly offer multiple shipping and cost options, and automate tracking updates so customers aren’t left guessing. If you can’t ship faster, look for ways to ship smarter. Fulfilling from the nearest warehouse to the destination and adjusting delivery windows by region, for instance, can help get products to your customers faster. At the very least, make sure to set clear expectations to reduce both uncertainty and the risk of churn.

12. Increasing Technological Complexities

    As ecommerce grows, so does the tech stack behind it—one tool for email, another for orders, something else for inventory. The more tools you add, the harder it gets to keep everything in sync. And without a centralized view of your operations and data, it’s easy for things to slip through the cracks, get duplicated, or break entirely. The result? Wasted time, inconsistent reporting, and teams working from different sources of truth.

    That’s why more ecommerce companies are turning to enterprise resource planning (ERP) systems to streamline and connect their processes. Instead of managing a patchwork of disconnected tools, you centralize everything—orders, inventory, customer relationship management, financials—in one place. In other words, it’s less about adding more software and more about building an environment of tools that actually talk to each other and work together, so your team spends less time chasing numbers and more time making decisions that move the business forward.

Strengthen Conversions With NetSuite SuiteCommerce

As ecommerce businesses grow, it gets harder to keep operations running smoothly, especially as customer expectations continue to climb. NetSuite SuiteCommerce helps bridge that gap by unifying ecommerce and back-end business operations for both B2B and B2C merchants. With workflows and data connected across the business, teams can spend less time troubleshooting and more time driving sales.

More specifically, NetSuite provides the tools to manage your entire online business from a single platform. This includes real-time visibility into orders, inventory, and customer data; support for multiple business models and sales channels; and flexible design tools that address the customer experience. It’s all built to streamline operations, reduce delays, and support smarter, faster decisions—ultimately helping businesses improve conversion potential.

Whether you’re just starting out or you’re already managing multiple storefronts, NetSuite SuiteCommerce can scale with your business so you can adapt to complexity, reduce operational friction, and deliver consistently better customer experiences as you grow.

Solving ecommerce challenges isn’t about fixing one part of the business, it’s about understanding how all the moving pieces connect. Issues, such as poor audience targeting, inefficient returns, rising customer expectations, and fragmented tech stacks, don’t exist in isolation. Each one affects all others, and, for better or for worse, together they shape the overall customer experience. The businesses that make real progress are the ones that prioritize strategy, clarity, and the right tools. They tend to adapt faster, respond with confidence, and deliver customer experiences that build trust and drive growth, bringing all the puzzle pieces into meaningful focus.

Ecommerce Challenges FAQs

How do you combat cart abandonment?

Reducing cart abandonment starts with simplifying the checkout process—think: fewer steps, clear calls to action, and multiple payment options. Transparent pricing and up-front shipping costs also help prevent last-minute surprises that drive customers away. Retargeting strategies, such as personalized emails or SMS reminders, can also re-engage shoppers who left items behind.

What are the major limitations of ecommerce?

Security concerns are paramount; inadequate safeguards can lead to data breaches that undermine customer trust. At the same time, the absence of tactile interactions inherent in brick-and-mortar shopping experiences means customers can’t physically assess products, potentially impacting purchasing decisions. Logistical challenges, such as shipping delays and complex return processes, can also hinder customer satisfaction. ​

What are some future trends in ecommerce?

Personalization is becoming more advanced, with AI enabling highly tailored shopping experiences founded upon individual behaviors and preferences. Mobile commerce continues to grow, making mobile optimization a top priority for brands. Sustainability is also influencing buying decisions, as more consumers seek out brands that prioritize eco-friendly practices. Additionally, augmented reality is transforming product discovery by creating opportunities that allow customers to visualize items in their own space, for example, before making a purchase.