Large corporates enter e-invoicing era as early birds flag hurdles

As the deadline for Nigeria’s electronic invoicing mandate ends today, the country’s largest corporations are discovering that adopting the technology is the easy part. Data quality, disjointed internal processes, and uncertainty over compliance requirements are emerging as the true compliance bottlenecks.

The new tax regime requires companies generating at least N5 billion in annual turnover to transmit invoices in real-time through the National Revenue Service’s Merchant Buyer Solution (MBS), enabling the government to tighten compliance and plug historic revenue leaks. While some large taxpayers are already transmitting invoices through the platform, others are still completing integration, testing, and validation ahead of the deadline.

For early adopters, the friction starts at the baseline of data entry.

“We went live before the deadline, and the integration has been seamless so far,” said Dapo Adeyemi, an ERP applications manager.

Despite the smooth rollout, Adeyemi said businesses are beginning to encounter operational challenges like customer data mismatches, which are triggering constant system rejections.

“The reality on the ground is that there is still some misalignment between the old Tax Identification Number (TIN) and the new Tax ID,” he said.

“There are cases where we receive a customer’s TIN, and when we transmit the invoice, it gets rejected because of the mismatch. We then have to go back to the customer to validate the information. Since the NRS allows only a 24-hour window to correct transmission failures, delays in getting responses from customers can become a challenge.”

He added that companies are continuing to engage with the tax authority as the system evolves.

A group head of tax at a leading Nigerian financial institution, who requested anonymity because he was not authorised to speak publicly, said his organisation had connected to the NRS network and questioned how large taxpayers would transact with suppliers that are yet to come under the e-invoicing mandate. Since small and medium-sized enterprises currently fall below the N5 billion threshold and remain outside the e-invoicing mandate, large corporates are seeking urgent regulatory clarity on how to legally process these offline invoices without running afoul of the new system.

Yele Oyekola, chief executive officer and co-founder of Duplo, said businesses should understand that compliance extends far beyond registration.

“Affected businesses should have completed onboarding on the Merchant Buyer Solution, integrated their systems through an approved Access Point Provider or System Integrator, completed validation and testing, and started transmitting invoices to the NRS platform,” he said.

“They should also review invoice data, VAT classifications, approval processes, and customer and supplier records to ensure the information being submitted is accurate. Registering on the platform without being able to issue and transmit compliant invoices does not amount to full compliance.”

Oyekola said one of the most common implementation mistakes is treating e-invoicing as solely an IT or tax project.

“It affects finance, procurement, operations, sales, and customer engagement. All these teams need to be involved in the implementation process,” he said, adding that businesses should also test how their systems handle rejected invoices, cancellations, credit notes, and high transaction volumes before going live.

Ayodapo Bamidele, a tax technology expert, agreed with Oyekola’s approach, noting that implementation challenges emerge long before companies begin transmitting invoices.

According to him, poor-quality financial records, incomplete invoice data, inaccurate tax determination, and invoice formats that do not align with the NRS standard are among the most common readiness issues businesses face.

He added that many organisations also underestimate the technical work involved, with finance and technology teams often requiring extensive support to understand invoice workflows and system integration.

“Integration could take up to three months, including readiness assessment,” Bamidele said, explaining that businesses expecting a quick technology deployment often overlook the operational changes required to achieve compliance.

Despite the implementation challenges, businesses say the long-term benefits outweigh the initial costs.

“I think it will simplify our tax administration process,” Adeyemi said.

“One of the incentives the NRS has provided is that once you’re compliant, claiming input VAT becomes easier because they have visibility into the transactions. That is a huge benefit.”

Oyekola said businesses also stand to reduce the time finance teams spend on manual reconciliation, payment disputes and audit preparation, while strengthening audit trails through more structured digital records.

As the compliance deadline approaches, experts advise companies still implementing the system to prioritise resolving integration issues, cleaning customer and supplier data, reviewing tax classifications, testing real transaction scenarios and training employees before going live.

They also urged medium-sized taxpayers not to wait for their own compliance timeline before beginning preparations, arguing that early planning would reduce implementation risks and allow businesses to adapt to a tax system that is increasingly moving towards real-time transaction reporting.