Implementing Transport Management in Microsoft Dynamics 365 can unlock significant efficiencies, improve cost transparency, and streamline logistics operations. But without the right approach, companies often underestimate their complexity, and that mistake can be costly.

Whether you’re a logistics leader, head of operations, or ERP manager, understanding the risks upfront is key to building a system that supports, rather than hinders, your supply chain. Based on insights from AlfaPeople experts, this article highlights common mistakes and guides on how to avoid them.

Underestimating the effort behind the setup

One of the most frequent mistakes companies make is assuming that Transport Management is a plug-and-play module. It isn’t.

Setting up transport rates, route plans, freight reconciliation, load structures, and carrier contracts requires both strategic planning and deep configuration. “There’s always an effort behind it,” notes AlfaPeople consultant Eries Shala. “But once it’s in place, most processes can be automated, and that’s where the real value begins.”

If your business handles shipments across multiple warehouses or works with both inbound and outbound flows, a significant setup effort is expected. Misjudging that effort can lead to partial implementations or frustration among internal teams.

Lack of shipment strategy or ownership

Transport Management isn’t just a system; it’s an operational mindset. Many projects fall short because no one takes actual ownership of the logistics structure or shipment planning process.

In companies where transport is treated as a side task, implementation often fails to deliver its full potential. As AlfaPeople’s Annette Ravn puts it, “It’s not something you do in a corner of the business. It must be an integrated part of your organization.”

Just as R&D departments own product structures, your logistics function needs a clear owner for route planning, carrier relationships, and freight cost strategy.

Missing the bigger picture

Another common issue is viewing Transport Management as an isolation. It sits at the heart of your broader logistics chain, interacting directly with warehouse operations, sales order management, and finance.

For example:

• If route plans aren’t correctly configured, shipments may fail during execution.
• If transport costs aren’t tied to customer pricing or sales orders, profit margins become unclear.
• If warehouse teams aren’t aware of routing structures, label mismatches or handling delays can occur.

To avoid these issues, your team must understand the entire shipment flow, from order creation and picking to final delivery and invoicing.

Configuration pitfalls: rates, routes, and responsibility

Incorrect configuration can derail even the best-intentioned projects. Some common technical missteps include:

• Missing route plans, leading to failed shipments or manual interventions.
• Rate setups not aligned with how carriers bill (e.g., per weight vs. per zone).
• No freight invoice reconciliation, which risks overpaying for shipments.
• Siloed configuration efforts across IT and logistics, without mutual understanding.

As McKinsey notes in a recent report on supply chain digitization, successful implementations require cross-functional collaboration to align technical systems with operational processes.

Start with a clear roadmap

The companies that succeed with Transport Management are those that invest time upfront to define:

• A shipment and routing strategy
• Ownership and responsibilities
• A phased configuration plan
• Carrier contract and cost frameworks
• Internal logistics flows and warehouse integration

By doing so, they avoid costly rework and instead build a solid, automated logistics backbone.

Final advice from the experts

Many businesses don’t realize what’s possible. “The biggest mistake is underestimating what the system can do,” says Eries Shala. “It’s not just about putting in routes; it’s about connecting costs, contracts, carriers, and execution into one seamless flow.”

Once implemented, the benefits are clear: reduced freight errors, more accurate pricing, better customer prioritization, and greater visibility from the warehouse to the final mile.

As supply chains become increasingly complex and margins become tighter, avoiding these pitfalls isn’t just smart; it’s essential.

Contact us for an informal meeting to learn how we can help you implement Transport Management effectively.