The Top Four e-Invoicing Implementation Challenges Businesses Face (And How to Overcome Them)

The global shift towards mandated continuous transaction controls (CTC) means that electronic invoicing (e-invoicing) is quickly becoming a strategic priority for businesses. Implementing a comprehensive e-invoicing system not only ensures compliance with local regulations but also improves operations and reduces costs over the longer term.

According to Vertex’s recent E-Invoicing Report research, 85% of businesses plan to improve the integration of their e-invoicing systems in the next two years. Investment in the right technology, which integrates with existing ERPs, enables smooth end-to-end workflows, automation, and real-time data insights.  

However, while the benefits are clear, implementation can be complex. From fragmented systems and data management challenges to internal adoption barriers, many businesses face hurdles on the path to e-invoicing maturity.  

Here, we’ll explore the top four challenges businesses have told us they face – and how to overcome them:

Challenge 1: Data Management

Strong data governance is essential for successful e-invoicing, but half of businesses report that data security and privacy are major challenges.  

As e-invoicing mandates increasingly require real-time validation and detailed reporting, businesses must ensure their data is clean, complete, and secure. Data quality inconsistencies and a lack of standardization can undermine compliance and reporting accuracy.

Regional differences in data laws and government support add another layer of complexity. A centralized, compliant e-invoicing platform, with a wide coverage of country-specific mandates, can help businesses manage these variations while maintaining control and transparency.  

Challenge 2: System integration

Integrating e-invoicing solutions with existing systems – particularly ERP systems – is one of the most common challenges that businesses face. In fact, 55% of businesses operating in mandated countries, and 63% selling internationally into countries that have local mandates, cite system integration as a key challenge.

Without proper system integrations, businesses risk mandate adoption delays, data inconsistencies, and compliance gaps that can impact both business operations and reporting accuracy. However, legacy technology, custom configurations, and siloed data can also be hurdles to implementing a seamless e-invoicing process.  

To overcome this, businesses should partner with an e-invoicing provider that offers implementation support, alongside flexible, API-driven solutions. A well-integrated system requires a tailored technical build and alignment with other financial systems and ERP environments to allow it to work seamlessly in the background.

Challenge 3: Internal Barriers and Costs

Cost remains a significant barrier to e-invoicing adoption, with 55% of businesses saying it is a concern. Initial investments in technology, training, and change management can seem high, especially when there are competing budget priorities. This challenge can be compounded by adoption hesitancy and a lack of understanding in the wider business.  

However, delaying implementation can lead to higher costs in the long-term due to inefficient manual processing and increasing compliance pressures as more countries introduce e-invoicing mandates. Businesses that invest in scalable, compliant solutions are better positioned to adapt to trading requirements and unlock operational savings.

Securing internal buy-in is key. Cross-functional understanding of the value of e-invoicing across tax, IT, and finance teams helps to ensure better collaboration, a smoother roll-out and a stronger return on investment.

Challenge 4: Diverse Jurisdictions and Compliance

Nearly 100 countries globally have now introduced e-invoicing mandates, and more are expected to in the near future. Each jurisdiction has its own rules, formats, and timelines, and there is currently no universal standard, making navigating global compliance a growing challenge.

For multinational businesses, this means managing multiple requirements that can change frequently. Staying compliant therefore requires constant monitoring, local expertise, and the ability to adapt quickly, especially when a piece-meal, manual approach to mandates is employed.

A global e-invoicing solution with real-time regulatory updates helps businesses stay ahead of changes and remain compliant. By centralising invoicing and automating updates, companies can reduce risk, simplify operations, and trade confidently across borders.

The Benefits of E-Invoicing Outweigh the Challenges

Ultimately, four out of five businesses agree that the value e-invoicing offers outweighs the implementation challenges they could face. While gathering the right data and aligning systems can be difficult without proper infrastructure, the long term-gains in efficiency, accuracy, and compliance are substantial. In fact, 81% of businesses believe e-invoicing enhances reporting and compliance capabilities.

With a clear strategy, cross-functional internal investment, and the right partner, businesses can move beyond compliance and unlock the full potential of a well-integrated digital tax transformation.

Read the full report to find out more!