Custom Software for Logistics: 5 Workflows Generic TMS Cannot Handle

Logistics is one of the most operationally-complex industries. Routing decisions, multi-modal coordination, real-time tracking, customer expectations of visibility, regulatory complexity per region — these requirements have grown faster than generic TMS (Transportation Management System) software has adapted.

For most logistics operators above ~50 vehicles or ~500 daily shipments, generic TMS software (Manhattan, Oracle TMS, MercuryGate, Descartes) starts becoming a constraint rather than an asset. Here are five workflows where custom beats generic.

1. Dynamic dispatch with rules per region

Generic TMS assumes a relatively static rule book. Real logistics ops have rules that vary by region, by carrier, by customer, by season, by time of day. A driver eligible for a route in one zone may not be eligible in another based on certification, vehicle compatibility, or customer requirements.

Custom dispatch engines model these rules as data, not code. Operations teams modify rules without engineering involvement. Generic TMS forces you to either fight the data model or pay vendor consultants for every rule change.

2. Multi-modal coordination

Most TMS handles one mode well — truckload, LTL, or air. When a single shipment involves multiple modes (truck pickup → ocean freight → truck delivery), the orchestration falls into spreadsheets, email threads, and manual coordination.

Custom TMS treats the full shipment lifecycle as one entity with modes as children, automatically updating ETAs as each leg progresses.

3. Real-time customer visibility

Customers expect Amazon-grade tracking. Generic TMS provides limited visibility, often through clunky portals that don't match the customer's brand.

Custom shipper portals (or even just custom track-and-trace pages) integrate with your TMS data, GPS/IoT feeds, and customer notification systems to deliver branded, real-time visibility. The marketing value alone often justifies the build.

4. EDI + API hybrid integration

Legacy customers want EDI (X12 850, 856, 210, 990). Newer customers want REST APIs. Generic TMS often handles one well and one poorly. Custom can natively bridge both — translating EDI to internal events that also flow to API endpoints.

5. Custom freight invoice reconciliation

Carriers invoice based on their interpretation of agreed rates. Your TMS calculates what you think you owe. Reconciling differences is manual, time-consuming, and frequently leaves money on the table.

Custom reconciliation engines compare expected vs invoiced rates automatically, flag discrepancies, and route disputes through workflow. Real number from one logistics client: $400k/year recovered in carrier overcharges in year 1.

What it costs

For logistics operators:

Lean dispatch + tracking ($60–120k): 50–500 daily shipments, 1–2 modes, single region. 10–14 week build.

Mid-market TMS replacement ($150–300k): 500–5,000 daily shipments, multi-modal, multi-region. Real-time tracking, EDI integration, customer portal. 16–26 week build.

Enterprise logistics platform ($350–800k+): 5,000+ daily shipments, full ERP integration, custom rate engines, freight audit, carrier scorecards, predictive ETAs. 24–40 week build.

When generic still wins

If you're under 50 vehicles or 500 daily shipments with relatively standard workflows, generic TMS is fine. Custom only pays back at scale or when operational differentiation matters.

For a transparent cost estimate for your specific logistics scope, our cost calculator takes 60 seconds. Or browse our 240+ products catalogue for related logistics apps.