Custom Software Development for E-Commerce
Order management, inventory, and fulfillment systems built for the multi-channel, multi-warehouse complexity that Shopify and generic platforms were never designed to handle.
E-commerce has a graduation problem. Most brands start on Shopify, and Shopify is excellent for getting to market quickly. But somewhere between $2M and $20M in annual revenue, the cracks start showing. Complex product configurations that Shopify variants cannot handle. Multi-warehouse inventory allocation that requires manual spreadsheet management. Wholesale and B2B channels that need different pricing, catalogs, and ordering workflows than your DTC storefront. International expansion that demands multi-currency, multi-language, and duty-aware checkout experiences.
The typical response is to bolt on more apps: an inventory management app, an order routing app, a subscription app, a B2B portal app. Each adds its own monthly fee, its own data silo, and its own integration headaches. Before long, you are paying $5,000 per month in Shopify apps to work around limitations that exist because Shopify is a storefront platform, not an operations platform.
Scale Labs builds the operational backbone for e-commerce brands that have outgrown their Shopify app stack. We create custom order management, inventory, and fulfillment systems that handle your specific product complexity, channel requirements, and operational workflows. Your storefront stays on Shopify (or migrates to a headless architecture), while your operations run on software built for how you actually sell and fulfill.
Common Challenges in ecommerce
Inventory Chaos Across Channels and Warehouses
Shopify, Amazon, wholesale, and your own warehouse each have a different view of inventory. Overselling on one channel while stock sits in another warehouse. Manual allocation spreadsheets that are outdated the moment they are created. No real-time visibility into available-to-promise across all channels.
Order Routing That Requires Human Judgment
Every order requires someone to decide which warehouse ships it, how to split multi-item orders, when to consolidate shipments, and how to handle backorder situations. These decisions follow rules, but your current tools cannot encode those rules, so your team makes them manually hundreds of times per day.
Product Complexity That Breaks Your Platform
Custom configurations, bundles, kits, subscription boxes with rotating products, and made-to-order items with customer-provided specifications. Shopify variants max out at 100 combinations, and your product model has thousands.
Disconnected Analytics and Reporting
Revenue in Shopify, ad performance in Google and Meta, inventory costs in your 3PL, and customer lifetime value calculated manually in a spreadsheet. Getting a unified view of profitability by product, channel, or customer segment requires assembling data from five different sources.
Why Shopify Apps and Generic OMS Tools Hit a Ceiling
The Shopify app ecosystem is remarkable for getting brands started, but it creates a specific architectural problem: every app is a separate system with its own database, its own sync schedule, and its own failure modes. When your inventory app, order routing app, subscription app, and wholesale app each maintain their own version of your product catalog and inventory levels, conflicts are inevitable.
Dedicated OMS platforms like Brightpearl, Cin7, and ShipBob's merchant tools solve some of these problems but introduce their own limitations. They are designed for common commerce patterns and struggle with the edge cases that define growing brands: subscription boxes with customizable product selections, B2B pricing tiers with negotiated contracts, made-to-order products with variable lead times, and international fulfillment with duty pre-calculation.
The deeper issue is that e-commerce operations are not generic. The optimal inventory allocation strategy for a fashion brand with seasonal collections and high return rates is completely different from an industrial supplier with stable demand and long lead times. No SaaS platform can optimize for both, which is why growing brands end up with a patchwork of tools that sort of work but never work well together.
What Custom E-Commerce Software Looks Like
Custom e-commerce software typically does not replace your storefront. Shopify, BigCommerce, or a headless storefront built with Next.js handles the customer-facing experience. What custom software replaces is everything behind the scenes: the order management, inventory allocation, fulfillment orchestration, and operational analytics that your app stack currently handles poorly.
A custom order management system takes orders from every channel (DTC, Amazon, wholesale, B2B portal) and routes them through your specific fulfillment logic. Inventory is allocated across warehouses based on rules you define: proximity to customer, warehouse capacity, stock levels, and shipping cost optimization. Split shipments, backorders, and exception handling follow your business rules automatically rather than requiring manual intervention.
Unified Order Management
A single system that processes orders from all channels with your specific routing rules, split shipment logic, and exception handling. Automated allocation, hold management, and fulfillment orchestration across warehouses and 3PLs.
Real-Time Inventory Allocation
Available-to-promise inventory calculated across all warehouses and channels in real time. Safety stock rules, channel-specific allocation, and automatic reorder triggers based on your demand patterns.
Profitability Analytics by Every Dimension
True profitability calculated at the order, product, channel, and customer level. Factor in COGS, shipping, returns, ad spend attribution, and payment processing fees to understand which products and channels actually make money.
How We Build E-Commerce Operations Software
E-commerce projects start with mapping your order lifecycle from placement through delivery and return. We document every decision point: how orders are validated, how inventory is allocated, how shipments are routed, how exceptions are handled, and how returns are processed. This mapping reveals the manual workarounds your team has developed and quantifies the time and error cost of each one.
We integrate with your existing storefront (Shopify, BigCommerce, or headless) and your fulfillment infrastructure (3PLs, in-house warehouses, drop-ship vendors). For channel sales, we connect to Amazon, Walmart Marketplace, and B2B EDI partners. The custom software sits between your sales channels and your fulfillment network, orchestrating the flow of orders and inventory data according to your business rules.
We build with scalability in mind because e-commerce traffic is inherently spiky. Black Friday, flash sales, and viral moments can generate 10 to 50 times your normal order volume. Our architectures handle these spikes without degradation, using queue-based processing and horizontal scaling to maintain performance regardless of volume.
The ROI of Custom E-Commerce Operations
E-commerce brands that implement custom order management and inventory systems see immediate operational improvements. Automated order routing eliminates the per-order manual processing time that limits scaling. For a brand processing 500 orders per day, eliminating 2 minutes of manual handling per order saves over 16 hours of daily labor. Real-time inventory allocation across channels reduces overselling incidents by 80 to 95 percent, directly reducing customer service costs and protecting your marketplace seller ratings.
The profitability impact is equally significant. Intelligent warehouse routing reduces average shipping cost by optimizing which facility fulfills each order. Unified inventory management reduces total inventory carrying costs by eliminating the safety stock buffers required when channels manage inventory independently. And accurate, real-time profitability analytics reveal which products, channels, and customer segments are truly profitable once all costs are factored in, enabling better decisions about where to invest marketing dollars.
What We Build for ecommerce
Multi-Channel Order Management System
Unified order processing for DTC, Amazon, wholesale, and B2B channels. Automated routing, inventory allocation, split shipment logic, and exception handling based on your business rules. Integrate with Shopify, Amazon Seller Central, and EDI partners from a single operational hub.
Custom B2B Commerce Portal
A wholesale ordering platform with customer-specific pricing tiers, negotiated contract terms, volume discounts, and net payment terms. Custom catalogs per customer, order approval workflows, and integration with your fulfillment and accounting systems.
Subscription Management Platform
Custom subscription logic that goes beyond simple recurring orders: curated boxes with rotating product selections, customer preference engines, skip/pause/modify workflows, and churn prediction analytics. Built for your specific subscription model rather than forced into Recharge's template.
E-Commerce Analytics and Profitability Dashboard
True unit economics calculated from order-level data: COGS, pick and pack costs, shipping, returns, payment processing, and attributed ad spend. Slice profitability by product, SKU, channel, customer cohort, and time period to understand where your business actually makes money.
Frequently Asked Questions
Do we need to leave Shopify to use custom software?
How does custom software handle peak traffic like Black Friday?
Can custom software integrate with our 3PL?
How long before we see ROI from custom e-commerce software?
Ready to Build the Operations Backend Your E-Commerce Brand Deserves?
Tell us about the inventory headache, order routing challenge, or channel complexity that your Shopify app stack cannot handle. We will design the operational system that scales with you.