Top Omnichannel Logistics and Supply Chain Challenges in Ecommerce (2026)

Your regular Tuesday shipment arrives at the warehouse. Meanwhile, a customer in Denver wants same-day pickup for an item showing "in stock" online. Another customer in Miami is returning a BOPIS order to a different store location. Your inventory system shows three different quantities for the same SKU across channels. Welcome to the reality of omnichannel logistics in 2026.

Managing inventory and fulfillment across multiple touchpoints isn't just complex—it's the difference between thriving and surviving in today's retail landscape. Shoppers expect to buy, receive, and return products anywhere, with the same seamless experience throughout. Making that happen requires orchestrating a symphony of supply chain processes, systems, and people that all need to work in perfect harmony.

This guide surfaces the eight biggest omnichannel logistics challenges retailers face in 2026 and provides the playbook to solve them.

What is omnichannel logistics?

Omnichannel logistics is how you orchestrate inventory and fulfillment across stores, warehouses, and carriers, so every channel can deliver the same promise to customers. It's the operational backbone that lets a shopper browse on their phone, buy on desktop, pick up in a brick-and-mortar store, and return via mail—all while experiencing one unified brand.

The key difference between multichannel and omnichannel logistics lies in inventory pooling and experience consistency. 

• Multichannel logistics treats each sales channel as a separate silo with dedicated inventory and independent operations. 
• Omnichannel logistics pools inventory into a single, shared source of truth that any channel can access, enabling a smooth order fulfillment process and seamless customer experiences.

Consider this typical customer journey: A shopper sees your ad on Instagram, researches on your website, checks store availability, orders online for curbside pickup, then returns one item in-store while keeping another.

In modern commerce, effective order fulfillment has become essential. Customer expectations continue to rise. Omnichannel retail used to be a nice-to-have for the biggest enterprise retailers, but it is now required to meet consumer demand for fast, free shipping and multiple touchpoints that get products in their hands sooner.

Supporting omnichannel fulfillment operations requires several interconnected systems:

• Order management systems (OMS) to route orders intelligently
• Warehouse management systems (WMS) for distribution center operations
• Point of sale (POS) for real-time store inventory and transactions
• Carrier integrations for shipping and tracking
• Returns management across all touchpoints

Curbside pickup was expected to account for $154 billion in sales in 2025. This shift to store-based fulfillment—like buy online, pick up in-store (BOPIS) and ship-from-store (SFS)—shows why true omnichannel logistics matters. Omnichannel shoppers spend 1.5x more each month than single-channel shoppers, per Deloitte's 2025 retail outlook.

Implementing omnichannel logistics sounds straightforward: Give customers what they want, when and how they want it. In practice, it creates distinct operational challenges that retailers need to understand and address systematically, from efficient order processing to AI-powered allocation to returns fraud prevention.

The eight biggest challenges brands face in 2026

There are many omnichannel logistics and supply chain management challenges retailers are wrestling with in 2026. Each represents a critical friction point within the distribution network where customer expectations meet operational reality.

1. Inventory visibility and pooling across channels

Inventory visibility and pooling form the foundation of omnichannel logistics. Without knowing what you have and where, every other promise becomes guesswork. The challenge isn't just seeing inventory levels; it's creating a shared pool that manages inventory flow and product availability that any channel can access, while maintaining accuracy down to the last unit.

Most merchants struggle with inventory spread across multiple distribution centers, stores, third-party logistics providers (3PLs), and dropshipping partners. Each location might use different systems or naming conventions. Your POS shows 10 units in-store, your ecommerce platform shows eight available online, and your actual count is seven. These mismatches lead to overselling, stockouts, and angry customers who were promised items you don't actually have.

The technical backbone requires understanding how modern systems work together. Your order management system (OMS) acts as the orchestration layer, pooling inventory data and making routing decisions. Distributed order management (DOM) takes this further, using algorithms to optimize which node fulfills each order. Your WMS manages distribution center operations with sales, inventory and operations planning (SIOP) to balance supply and demand. Your POS handles store-level inventory management with real-time updates critical for available-to-promise (ATP) calculations.

ATP logic determines what's actually sellable. If you have 100 units but need 20 for safety stock, 10 for subscription orders, and five for VIP customers, only 65 are truly available. Modern ATP engines calculate this in real time, considering factors like incoming shipments, returns in transit, and channel-specific buffers.

💡Tip: Track top-performing SKUs across different sales channels, retail stores, and geographic locations with Shopify. The unified data model funnels all key data back to one place, which you can use to populate more than 60 premade reports or create custom data exploration. 

2. Store-based fulfillment readiness

We know distribution centers operate primarily as fulfillment hubs. But what about your retail locations?

Store-based fulfillment is now table stakes, not a nice-to-have for forward-thinking retailers. BOPIS, curbside pickup, ship-from-store, and buy online, return in-store (BORIS) have shifted from pandemic conveniences to permanent expectations. Yet most stores weren't designed for fulfillment—they were built for browsing.

The operational challenges are immediate and tangible. Where do online orders get staged without blocking customer traffic? How do associates pick items while also helping in-store shoppers? Who handles curbside runners during peak hours? What happens when the last unit on the shelf is claimed both online and in person simultaneously?

A 2024 Forrester survey showed that half of US adults used store pickup for some portion of their online orders within the prior three months, illustrating the massive operational load stores now carry. This isn't an edge case—it's core to how customers shop and how retailers meet demand. BORIS adds another layer, with online purchases returning through store locations, requiring staff training on different return processes and impacting store inventory unexpectedly.

3. Delivery-date promise and speed

Shoppers care more about reliable delivery dates than raw speed—they want to know when their order will arrive and have that promise kept. The challenge is translating your actual network capabilities into accurate, dynamic promises that vary by customer location, inventory position, and carrier performance.

Your delivery promise starts with network design: where inventory sits and how it flows to customers. More nodes don't automatically mean better service. Each additional location adds complexity. Synchronizing inventory flow is crucial because spreading inventory too thin can hurt availability. Regional distribution centers, store fulfillment, 3PL partnerships, and dropship arrangements all need to work as one coordinated network.

Last-mile delivery accounted for 53% of total shipping costs in 2023, up from 41% in 2018, according to the World Economic Forum. This cost pressure makes network optimization critical. AI-powered routing engines now consider dozens of variables: carrier performance by lane, seasonal patterns, capacity constraints, and even weather impacts.

💡Tip: Shopify Fulfillment Network connects your store with Flexport, a leading logistics provider, to manage outsourced fulfillment directly from your Shopify admin. Inventory, order, and customer data sync across systems for real-time insight into DTC fulfillment. 

4. Reverse logistics and returns economics

Reverse logistics is now a major profit lever, not an afterthought in your fulfillment strategy. Retailers estimated that 15.8% of their sales would be returned in 2025, totaling approximately $849.9 billion. Returns abuse and fraud account for roughly 9% of returns, according to the National Retail Federation. These are more than just operational headaches—they're real threats to margins.

BORIS flows present both opportunity and challenge. Online orders returned to stores eliminate return shipping costs and create cross-selling opportunities. However, they also burden store associates with more complex processing steps. They can also distort store-level inventory planning when a location suddenly receives returns for items it never stocked.

5. Allocation and order orchestration

Modern allocation uses AI-assisted routing and sophisticated orchestration rules that balance cost, speed, and inventory health in real time. Distributed order management (DOM) systems now make split-second decisions about which fulfillment node should handle each order based on complex algorithms.

The orchestration challenge has evolved beyond simple "ship from closest location" logic. AI engines consider inventory aging, labor availability, carrier capacity, weather patterns, and even sustainability impacts. An order might route to a farther location because inventory there is aging, the closer store is understaffed, or consolidating with another order reduces shipping costs.

Cross-border complexities add another layer for retailers selling internationally. Duties, taxes, restricted items, and carrier capabilities must factor into routing decisions. Some nodes can't ship internationally, others have preferential rates for specific countries, and certain products face import restrictions.

Return on investment (ROI) trade-offs become critical as the complexity of order orchestration increases. Advanced DOM systems can optimize perfectly but require significant investment and dedicated resources. Small and medium-size businesses (SMBs) must balance orchestration benefits against implementation costs, often starting simple and adding intelligence gradually.

⭐ To level up: Add order-routing rules across multiple fulfillment centers to balance cost vs. speed while maintaining customer satisfaction.

6. Last-mile routing and tracking

The last mile is where most cost and customer perception live: routing efficiency and tracking visibility determine whether your delivery promise feels trustworthy or leaves customers anxious. This final leg from distribution point to doorstep shapes the entire order experience.

The challenges are both operational and experiential. Operationally, you need to optimize routes for efficiency, batch orders intelligently, and handle the complexity of delivery windows. Experientially, customers expect real-time visibility, proactive delay notifications, and proof of delivery. When a package shows “out for delivery” for hours with no updates, customer anxiety spikes and support tickets flood in.

Up to 19% of logistics costs stem from inefficient handover interactions, amounting to up to $95 billion in losses annually in the US alone, according to a McKinsey analysis. Handover frictions—between your warehouse and carriers or carriers and customers—create both cost and experience problems.

7. Tech stack integration and data quality

Omnichannel logistics breaks when systems don't talk. Integrated data is what makes promises accurate and operations scalable. Yet most retailers operate with a patchwork of systems held together by spreadsheets and manual updates. This creates lag, errors, and blind spots that cascade into customer problems.

Your tech stack likely includes Shopify as your commerce platform, a POS system for stores, potentially an OMS for order routing, WMS for warehouse operations, various carrier integrations, and possibly an enterprise resource planning platform (ERP) tying it all together. Each system might use different SKU formats, name locations differently, or update on different schedules. When your POS says "Main Street Store" but your OMS calls it "Location 003," integration breaks.

Data quality issues compound quickly. Duplicate SKUs mean inventory gets split incorrectly. Mismatched location codes prevent ship-from-store. Delayed updates cause overselling. Manual data entry introduces errors that take weeks to surface. These aren't just technical annoyances—they directly impact your ability to fulfill orders accurately.

Shopify provides a strong foundation with unified inventory and fulfillment data across channels. The Shopify App Store offers prebuilt integrations with major WMS, OMS, and 3PL systems. For enterprise systems, Shopify's Global ERP Program provides certified connectors that maintain data fidelity.

The goal isn't perfection, but consistency. Your systems should share a common understanding of what you're selling, where it lives, and how it moves. This shared language enables the real-time coordination that omnichannel logistics demands.

8. Labor, sustainability, and cost-to-serve trade-offs

Every omnichannel retail decision has labor and environmental costs. Leading brands design networks that balance speed, cost, and sustainability rather than optimizing for any single dimension. These trade-offs become more complex as customer expectations rise while margins compress.

Labor constraints hit from multiple angles: 

• Store associates now pick online orders while serving customers. 
• Distribution centers need skilled workers for increasingly complex operations. 
• Peak seasons require temporary staff who need training. 

Each fulfillment method has different labor requirements: BOPIS needs pickers and runners, ship-from-store requires packers, and curbside demands coordinators. You can't just toggle on new fulfillment options without considering who will execute them.

Sustainability pressures mount as consumers and investors demand environmental responsibility. Split shipments might arrive faster but double packaging waste. Daily deliveries increase emissions versus consolidated weekly drops. Returns generate enormous waste—returned items often can't be resold at full price and packaging rarely gets reused. Yet customers still expect fast, free delivery and easy returns.

Cost-to-serve analysis reveals uncomfortable truths. That free two-day shipping (or even next-day delivery) on a $15 order? You're losing money. Free returns on commodity items? Also unprofitable. BOPIS for single items during peak hours? The labor cost exceeds the margin. Without understanding unit economics, you can't make informed trade-offs.

How leading brands solve these problems

Even smaller brands can borrow patterns from industry leaders—you don't need Amazon-level infrastructure to implement these proven approaches. The key is choosing one or two patterns to pilot first rather than attempting everything simultaneously.

Supply chain professionals and leading brands focus on five core areas: network design that matches demand patterns, service-level agreements (SLAs) that reflect true capabilities, store operations that support fulfillment, returns flows that recover value, and last-mile instrumentation that builds trust. Each area offers specific practices you can adapt to your scale and resources.

Design the network

Start with the physical network—where inventory sits and how it flows—to meet promises without overspending. Your network design determines every downstream capability from delivery speed to return options.

Network nodes come in various forms, each with trade-offs:

• Central distribution centers (DCs) offer economies of scale, but increase average delivery distance.
• Regional DCs reduce transit time, but split inventory.
• Store fulfillment provides speed, but requires operational changes.
• Micro-fulfillment centers in urban areas enable same-day delivery, but only for limited SKUs.
• 3PL partnerships provide flexibility, but reduce control.

Be sure to resist the temptation to overcomplicate. You don't need 20 distribution points to compete effectively. Focus on right-sizing your network for actual demand patterns, not theoretical coverage. A single DC plus ship-from-store in key markets can often outperform a complex multi-node setup that spreads inventory too thin.

Map your path forward:

• Analyze current order density by region to identify where you actually need inventory.
• Overlay this with your existing facilities (stores, DC, 3PL partners) to spot gaps and redundancies.
• Decide whether to fill gaps via 3PL partnerships or store fulfillment before considering new facilities.
• Set stocking strategies to determine which SKUs live where based on velocity and demand patterns.

💡Tip: Shopify’s unified data model brings together your order, customer, and inventory data into a centralized operating system. This acts as a single source of truth for every stage of DTC fulfillment. 

NZXT, for example, cut fulfillment times from 10 days to under two after simplifying configurations and processes on their ecommerce platform, demonstrating how technology integration drives improvement.

Set channel SLAs and a dynamic promise

Translate your network capabilities into clear promises by channel, then surface them as dynamic delivery dates that build trust. Your service-level agreements should reflect what you can actually deliver, not what you hope to promise.

Different channels demand different SLAs. Marketplaces often require two-day delivery to maintain seller ratings. Your website can offer more flexibility with economy and express options. Wholesale might accept longer lead times but require precise delivery appointments. Each channel's requirements should map to your operational capabilities.

Dynamic promises show customers accurate delivery dates based on their location, chosen items, and current capacity. Instead of generic "3–5 business days," show "Order within 2 hours for delivery by Thursday, January 23." This specificity drives conversion—customers trust concrete dates over vague ranges.

Implement realistic SLAs:

• Define baseline capabilities like same-day pick, next-day ship, and standard transit times by zone.
• Map these to channel requirements ensuring you can meet marketplace mandates.
• Use Shopify's delivery promise features or carrier APIs to calculate real-time delivery dates.
• Monitor promise accuracy weekly and adjust buffers when you consistently miss or exceed targets.
• Underpromise slightly so you can consistently deliver on time.

Operationalize store fulfillment

Turning stores into mini-warehouses requires new inventory-optimization workflows, not just a ship-from-store toggle in your software. Successful store fulfillment demands thoughtful process design, staff training, and continuous refinement.

Store associates face competing priorities. A customer needs help finding sizes while online orders pile up for picking. The curbside alert sounds during a checkout rush. Returns processing backs up during peak shopping hours. Without clear procedures and appropriate staffing, service levels suffer across all channels.

Pilot your approach gradually. Choose high-volume stores with strong managers and start with BOPIS only. Once pickup flows smoothly, add ship-from-store for nearby ZIP codes. Finally, enable customers to get their orders through curbside and same-day delivery. This phased rollout lets you refine processes without overwhelming staff.

To build store fulfillment capabilities, transform stores into fulfillment nodes with detailed picking flows:

1. Pick optimization:

• • Select pilot stores based on order volume, space availability, and management strength.
  • Implement batch picking for multiple orders to minimize floor time.
  • Use zone picking where associates handle specific departments.
  • Create pick paths that avoid high-traffic areas during peak shopping.
  • Deploy handheld devices showing optimized pick sequences.

2. Pack and stage workflows:

• • Design the physical workflow covering pick paths, staging zones, and customer handoff points.
  • Designate packing stations away from customer areas.
  • Implement quality checks including barcode scanning for accuracy.
  • Create staging zones organized by pickup-time slots.
  • Consider warehouse automation tools to optimize your packing and staging workflows.
  • Establish carrier pickup schedules that don't block receiving.

3. Labor allocation models:

• • Train staff in phases starting with order picking, then packing, then customer interaction.
  • Calculate labor standards: picks per hour, pack rates, handoff times.
  • Staff dedicated fulfillment associates during order peaks.
  • Cross-train sales associates for surge capacity.
  • Monitor productivity metrics to refine staffing models.

4. Loss prevention and returns integrity:

• • Implement cycle counting for high-velocity SKUs to maintain inventory accuracy.
  • Verify BORIS items against original orders before accepting.
  • Check for returns fraud indicators (wrong items, excessive wear, missing components).
  • Grade returned items immediately: restock, markdown, or defect.
  • Track store-level shrink patterns related to omnichannel operations.

Finally, track performance metrics: pick rate, accuracy, ready times, and customer satisfaction.

One successful approach: dedicate morning hours to fulfillment before stores open. Associates can pick and pack without customer interruption, orders get staged for the day, and inventory counts stay accurate. This “fulfillment first” model treats online orders as equally important as walk-in sales.

Tighten returns flows

Leading brands treat returns as a designed flow—from policy through disposition—not an ad hoc headache. Every return touchpoint should be optimized for efficiency and value recovery.

Start by understanding your specific returns patterns. Which products come back most? Which channels generate the highest returns? What percentage can be restocked at full price? These insights inform policy decisions.

Brick-and-mortar returns processing determines value recovery. In-store returns should flow through dedicated areas with clear grading criteria. Items rated A get restocked immediately. B items might need repackaging. C items go to clearance. D items get liquidated or donated. A systematic approach maximizes recovery while minimizing handling time.

To create an efficient returns system:

• Calculate returns rates and costs by product category using actual processing expenses.
• Design policies that align with economics such as free returns for high-margin items, fees for commodities.
• Establish in-store returns areas with scanning stations, grading guides, and disposition routing.
• Identify partners for refurbishment, liquidation, and donation to handle non-restockable items.

Consider incentivizing store returns over mail-in. Provide customers with instant refunds for store returns while mail-in takes 7 to 10 days. This reduces shipping costs, drives store traffic, and creates cross-selling opportunities. Train associates to process returns quickly while remaining approachable—a smooth returns experience builds loyalty even when products disappoint.

Instrument the last mile

Instrumentation—alerts, delivery windows, proof of delivery—transforms last-mile from a black box into a controllable experience. Visibility builds trust while reducing support burden.

Customer anxiety peaks during delivery. After clicking "Buy," they wonder: Did it ship? Where is it now? Will someone need to sign? What if I'm not home? Proactive communication answering these questions prevents support tickets and builds confidence for future purchases.

Modern carriers provide APIs for tracking events, but raw carrier messages often confuse customers. “Departed facility” means nothing to someone expecting their package today. Translate carrier updates into clear, branded communications that set accurate expectations.

Build last mile visibility:

• Enable all carrier notification options and customize messages with your brand voice and support contact.
• Implement real-time tracking for local delivery showing driver location and estimated arrival.
• Capture proof of delivery including photos and signatures to resolve disputes quickly.

For local delivery from stores, instrumentation becomes even more critical. Customers choosing same-day delivery expect Amazon-level visibility. Show them when their order gets picked, when the driver departs, and live tracking to their door. This transparency justifies premium pricing while reducing “Where is my order?” calls.