Integrating FAP and TMS: a smarter approach to freight spend management

For supply chain leaders, transportation is a lever for operational resilience, customer satisfaction and competitive advantage.  

But even the best routing strategies and carrier negotiations fall flat if freight costs aren’t properly audited and managed after the shipment leaves the dock. 

That’s where many organizations still struggle.  

When Freight Audit and Payment (FAP) is siloed from Transportation Management the separation creates   fragmented processes, overpayments and poor visibility into spend.  

The good news?  

Integrating FAP and TMS is one of the most underutilized ways to transform freight spend into a strategic advantage. 

In this blog, we explore why integrating FAP and TMS is key to reducing transportation spend and how it can unlock greater visibility, efficiency and strategic insight across your supply chain. 

Your freight spend is out of sync and it’s costing you

Disconnected systems between finance and logistics are not just a nuisance; they’re expensive. When invoices are handled manually, with limited context from operations, the result is:

• 3x higher operational costs when audits are manual vs. automated (Gartner)
• 60+ day payment delays caused by invoice disputes
• 30% of freight payments arriving late through legacy systems (JP Morgan)
• Wasted time chasing exceptions, reconciling invoices and validating rates line-by-line

This translates to lost team bandwidth, strained relationships and money left on the table. As volumes grow and networks expand, this is no longer sustainable.

Why built-in TMS auditing isn’t enough

Many TMS platforms offer basic freight audit features. But these tools rarely scale to support enterprise-level freight control and complex transportation networks. They can validate rates;  for example, did the invoice match the carrier quote – and flag discrepancies, but they fall short in key areas:

• No detailed cost allocation across GL codes, SKUs or regions
• No robust dispute resolution or claims handling
• No support for parcel overcharge recovery or credit tracking
• No automation of freight accruals for unbilled shipments
• Limited ability to inform procurement and carrier strategy

Without a dedicated FAP platform, finance teams struggle to get the spend visibility they need, while logistics leaders lack the insight needed to make cost-effective decisions.

The case for a dedicated FAP solution

A modern FAP platform is a strategic operations asset and more than a financial tool that delivers capabilities including

• Automated audit workflows across all modes and carriers
• Exception handling and carrier disputes managed by the FAP provider
• Accurate, granular GL coding and accrual tracking for cost visibility and cleaner period-end reporting
• Parcel credit recovery and claim resolution
• Spend dashboards and benchmarking for smarter sourcing decisions

In short, a modern FAP solution gives you the tools to drive smarter decisions at the network level, in addition to avoiding overpayments. 

Did you know?

According to our data, shippers leveraging integrated FAP have reduced transportation spend by 7–10% annually just through improved data visibility and network optimization.

Why integration with TMS matters: a maturity curve for freight optimization

FAP and TMS each add value. But when integrated, they transform your ability to manage transportation holistically; from planning and execution through to cost reconciliation.

 Integration isn’t binary; it evolves. 

When FAP is seamlessly integrated with your TMS, you get:

• Real-time cost visibility without waiting on finance
• Less time spent chasing disputes and reconciling invoices
• Fewer errors, fewer payment delays and stronger carrier relationships
• Clear insights that help improve mode mix, routing and carrier strategy
• More team bandwidth to focus on execution, not back-office tasks

Here’s what the FAP + TMS integration journey typically looks like from an operations perspective:

Level 1: standalone FAP 
Automates invoice validation and payment, freeing internal teams from manual checks.

Level 2: FAP Integrated with third-party TMS 
Links shipment execution data to audit and payment processes. Enables granular cost allocation by order, customer, lane or SKU and supports accurate, automated accruals.

Level 3: unified solution (Same Vendor) 
Combines operations and financial intelligence in real time. Routing logic, cost anomalies and overcharges inform strategic adjustments across the network; closing the loop between plan, execution and payment.

This last stage of a unified solution is where Infios delivers the most value: by combining its TMS and FAP into a single, cloud-native platform, teams gain real-time visibility, rapid dispute handling and full cost visibility - all in one place. 

5 signs it’s time to re-evaluate your FAP strategy

Not sure if you’re ready to upgrade? Here are five red flags: 

Ask yourself:

• Are your internal teams overwhelmed by invoice audits?
• Do you struggle to understand cost breakdowns by product or region?
• Are your TMS and finance systems operating in silos?
• Are you dealing with disputes that drag out for weeks or months?
• Do you lack real-time insight into your transportation spend?

If you’re nodding to any of these, it’s likely time to evolve your freight audit strategy.

Freight spend management is a strategic lever, if you integrate it 

Transportation spend audits shouldn’t be a reactive process handled after the fact.  When FAP and TMS operate in sync, you don’t just reduce cost; you build a smarter and more responsive supply chain. 

Whether you're scaling across geographies, manage multimodal networks or look to increase operational efficiency, integrating FAP and TMS is one of the most immediate ways to reduce cost, improve visibility and empower your teams.