A successful Transport Management implementation in Dynamics 365 can dramatically improve your logistics efficiency, cost transparency, and end-to-end control. But implementing it requires more than just enabling a module; it demands strategic planning, process alignment, and cross-functional collaboration.

To help you get started, we’ve gathered seven practical tips based on insights from AlfaPeople consultants who work hands-on with Transport Management in Microsoft Dynamics 365. Whether you’re just considering implementation or already in the planning phase, these tips will help ensure a smoother journey.

1. Align with your logistics structure before configuring

Before diving into setup, define your logistics model. How many warehouses do you operate? Which routes are standard? How do goods flow from a sales order to a shipment? “Transport Management must reflect your actual logistics structure, not the other way around,” notes AlfaPeople consultant Eries Shala. For businesses with complex routing and multi-warehouse operations, a well-defined process is essential for configuring transport flows that scale effectively.

2. Assign clear leadership, don´t let it fall between departments

Successful ERP implementations always involve ownership. Just as R&D manages bills of materials (BOMs), someone must own your transport structure, rate agreements, and carrier relationships.

“If no one owns shipment planning, route updates, or label management, it quickly breaks down,” explains AlfaPeople’s Annette Ravn. Assign cross-functional roles across logistics, operations, and IT early in the process.

3. Automate wherever possible

Dynamics 365 provides automation for shipment creation, load planning, route assignment, and label generation. Once the system is configured, much of the heavy lifting can be handled in the background.

“After setup, processes flow automatically,” says Shala. “That’s where the real efficiency is unlocked.”

Automation helps reduce manual errors, allowing your teams to focus on higher-value tasks. Configure batch jobs and automated workflows to maximize the value of your investment.

4. Link transportation costs directly to sales orders

With the correct setup, Transport Management allows you to assign freight costs to specific sales orders, customers, or order types, making cost control more transparent and pricing more accurate.

This integration with trade agreements also enables customers to be charged automatically based on distance, weight, or predefined zones. That level of precision can support both profitability and customer satisfaction.

5. Use postal zones, freights, and mileage for flexible rate logic

One of the system’s strengths is its ability to handle highly customized freight calculations. Whether you bill by the kilometer, by weight, or by zone, Dynamics 365 can support it.

“You can define fuel indexes by region, or set rates for specific postal codes,” says Shala. “It’s flexible—but it must be configured carefully.”

Plan your pricing logic and work closely with your carrier contracts to ensure they align.

6. Use the freight invoice reconsiliation tool

Errors in freight billing are more common than most companies expect. Fortunately, Dynamics 365 includes a built-in reconciliation tool that checks actual charges against agreed rates and shipment data.

According to a study by ARC Advisory Group, companies using TMS solutions with invoice auditing capabilities reduce freight billing errors by up to 95% (ARC – Transportation Management Benefits). Don’t overlook this feature; it can protect both your margins and your vendor relationships.

7. Train all relevant departments, not just logistics

Transport Management touches more than just the warehouse. Sales, finance, and even customer service need to understand how shipments are calculated, tracked, and costed.

“People often assume it’s a logistics-only setup,” says Ravn. “But you need everyone to speak the same language.”

Conduct training workshops to align teams on how the system works and create comprehensive documentation for future reference. The more people understand the full transport flow, the better your implementation will perform.

Final thoughts

A well-executed Transport Management implementation can reduce errors, accelerate delivery times, and give your business a more strategic grip on freight expenditure. However, it requires a solid foundation: clear ownership, automation, accurate costing, and system-wide alignment.

Take the time to plan it right, and don’t hesitate to bring in experienced consultants to guide the process.

Contact us to arrange an informal meeting and explore how AlfaPeople can support your Transport Management implementation in Dynamics 365.