The Complete Guide to Transportation Management System Implementation: From TMS Setup to Go-Live

For shipping leaders evaluating a new Transportation Management System (TMS), the decision often stalls on one question: What if the transition disrupts our operations?

It's by far the #1 concern we hear. You're managing thousands of shipments, coordinating dozens of carriers, and keeping customers happy with on-time deliveries. The idea of swapping out the system that orchestrates all of this can feel like changing an engine mid-flight.

After hundreds of implementations across food and beverage, automotive, manufacturing, and distribution, we’ve learned the difference between a painful transition and a seamless one isn't luck—it's methodology. When you choose a partner with a proven, phase-based approach, TMS implementation becomes less about risk and more about unlocking value faster. Here’s what that actually looks like.

What Makes for a Smooth Transportation Management System Implementation?

After hundreds of projects, we've identified the patterns that predict success. The smoothest implementations share four characteristics:

1. Documented workflows and requirements‍

When organizations have their workflows documented and know their business requirements, they are better prepared to evaluate their future state and manage the change that comes with moving to a new platform. Targeting specific business needs, and having the ability to evaluate the new workflows can help focus on the most important operational requirements and make sure these are addressed in the solution.

2. Early engagement of the right stakeholders

‍Executive buyers focus on ROI and strategic outcomes. Operations teams focus on daily workflows and exception handling. IT leaders focus on integration architecture and security protocols. When all three groups understand the priority, transitions are made easier. 

3. Aligned expertise

Strong project management keeps timelines on track and ensures accountability across teams–but it's when a PM has access to the overall project team AND subject matter experts (SMEs) that the real magic happens. The difference between a project that drifts and one that delivers is a collective, critical effort in assessing the proposed solution against business workflows.

4. Exceptional, intentional communication

Having the right people on board and informed ensures everyone is on the same page and stays that way, regardless of project phase. By scheduling regular check-ins, it's easier to build momentum and prevent frustration from compounding.

The ROI of Getting Implementation Right

Let's talk numbers. When implementation is done well, you see three types of value:

• Faster go-live: Structured methodology and clear ownership keep projects on schedule. Most customers go live in just 12 to 14 weeks.
• Quicker time to value: Clean data, validated workflows, and comprehensive testing mean you realize ROI sooner. Companies typically see measurable savings within the first year through automated routing guides and spot bid optimization.
• Long-term operational gains: Automation compounds over time. Customers report reclaiming hundreds—sometimes thousands—of hours annually through automated planning, spot market efficiency, and settlement processes. Instead of one-time wins, they're structural improvements that free teams to focus on strategy instead of spreadsheets.

The Six Phases That Turn Chaos Into Clarity

A successful  transportation management system implementation isn't a single event; it's a structured journey. At Shipwell, we break it into six phases, each designed to build momentum and increase operational readiness.

Phase 1: Prepare & Kick-Off

This is where alignment happens. We confirm the scope, introduce your team to ours, and establish clear ownership on both sides. You'll meet your Solution Consultant, Project Manager and Customer Success Manager (CSM)—the people who will guide you from contract signature through go-live and beyond. 

Integration endpoints and API documentation are reviewed upfront, so IT leaders and their technical team know exactly what to expect. No surprises three weeks in. We’ll also help you to identify your super users—the people who will own operational requirements, validate configurations, and train end users. 

Phase 2: Design

Taking the newly-created scope requirements and the current state information uncovered during the sales process, we start to imagine what workflows could look like in the new TMS. Looking at the entire order to cash workflow with SMEs and Superusers, we discuss:

• How new workflows could align to the business requirements
• Areas for improvement and efficiency gains
• Where additional change management exercises may be needed

The output of this phase is a document that serves as a baseline for how the customer will use their new TMS and a basis for agreement on “what good looks like.” It also provides the foundation for building test scenarios, standard operating procedures (SOPs), and ensuring the enablement of better customer service down the road by having a record of their TMS workflow design.

One beverage manufacturer we worked with had been managing 16,000 annual FTL shipments across five distribution centers using a patchwork of spreadsheets and email. During the design phase, we documented their routing guide logic, spot bid processes, and carrier communication preferences. By the end of week four, they had a blueprint for automating 80% of their freight decisions.

Just imagine what kind of efficiency gains we’ll uncover for you.

Phase 3: Build

Now we configure the TMS setup in a sandbox environment—a safe space to test without touching your live operations. Master data gets validated (customers, carriers, locations, contracts, lanes). Integrations get developed. Carriers get connected.

Here's where Shipwell's carrier platform becomes a differentiator. Not every carrier has the same technical capabilities. Some are EDI-only and won't log into shipper portals. Others are regional mom-and-pops who prefer email. We accommodate everyone, so you don't lose visibility or compliance.

An automotive parts manufacturer connected 33 carriers—10 via EDI, the rest through our mobile app and carrier portal. The flexibility meant they could onboard their entire network without forcing carriers into workflows they couldn't support.

Phase 4: Test & Train

User Acceptance Testing (UAT) is where theory meets reality. We provide a test script template, but you add the edge cases specific to your business. You’ll need to have answers to questions like: 

• What happens if a carrier misses a pickup? 
• How do you handle multi-stop FTL shipments? 
• What if a customer changes delivery instructions mid-transit?

Training happens in parallel—role-specific sessions for planners, dispatchers, carrier relations teams, and finance. We don't just show people where to click; we explain why the system is configured the way it is.

A beef purveyor ran 100% of their volume through spot markets. During UAT, they tested automated spot bidding across 15 carriers, allowing four hours for responses. The result: $500,000 in annual cost avoidance and 750 hours saved in spot market efficiency.

Phase 5: Go-Live & Hypercare

On the agreed upon day, we “cut-over,” meaning we flip the hypothetical switch so that orders start flowing through your new TMS setup. Every step of the way, our team helps guide you, whether it is a single phase or gradual roll out (all-at-once, by site or by mode,) to ensure the solution meets the needs of your business.

But we don’t disappear on day 1. During the hypercare window, two weeks post go-live, our team provides rapid-response support—immediate calls, not ticket queues. If something feels off, we address it before it becomes a problem.

When leading meal kit delivery service Home Chef realized they were scaling faster than their current process could support, they sought to find a logistics partner that could help them both retain their outstanding customer service record and keep costs under control. Shipwell assured deployment within three months and did so with zero operational fires on day one because we'd tested every workflow, trained every user, and validated every integration.

Phase 6: Customer Success Transition

After hypercare, your CSM—who you met at the very beginning of the TMS implementation–will continue to check in with you to see how things are going. They’ll show you the support portal, align on new opportunities or value-added features, and discuss new platform capabilities as they're released.

A $2 billion automotive manufacturer started with FTL and later added dock scheduling across five facilities. Within months, they were scheduling 4,000 appointments in-platform and achieving 100% on-time delivery with top carriers.

{{divider}}

Transportation management system implementation isn't inherently risky—but choosing the wrong partner is. When you work with a team that has a documented methodology, transparent communication, and a track record of delivering results, implementation becomes the foundation for long-term success.

You don't need a massive internal team. You don't need to halt operations. You just need clarity on your workflows, engagement from the right stakeholders, and a partner who's done this hundreds of times before.

Because at the end of the day, the goal isn't just to go live. It's to go live with confidence, realize value quickly, and build a supply chain that scales with your business.