Beyond results on the pitch, the NFF has faced questions over governance and financial management.
Particular attention has focused on a 17bn naira ($12.66m, £9.31m) intervention fund reportedly approved by Nigerian President Bola Tinubu in 2024 to settle outstanding payments and obligations owed to the country’s national teams.
While no formal findings have been announced, sources familiar with ongoing reviews describe the process as an examination of financial documentation and administrative procedures.
Meanwhile, a fact-finding committee set up by the NFF after Nigeria’s Wafcon 2026 exit highlighted a number of issues at board level and in the organisation of national teams.
Its report included allegations that NFF board members influence team selection and that officials and even coaches base call-ups for players on financial gain as opposed to performance.
Discussions at the upcoming emergency congress are expected to focus on the status of the executive committee and compliance with statutes of the NFF, the Confederation of African Football, and world governing body Fifa.
The current uncertainty casts doubt over NFF elections scheduled for September. The possibility of a Fifa-backed normalisation committee to oversee the transition and prepare for fresh elections has been mooted.
Calls for sweeping reforms have grown louder in recent months.
Former Nigeria internationals including John Obi Mikel, Jay-Jay Okocha and Segun Odegbami have publicly argued that meaningful progress will require a complete break from the cycle of familiar administrators who have overseen years of underperformance.
And while the resignations create uncertainty, some stakeholders believe the crisis could also present an opportunity for long-awaited structural reforms and a cultural reset.
The upheaval comes against the backdrop of wider discussions over governance and accountability within global football, with Fifa boss Gianni Infantino at the heart of the debate.
For Nigeria, however, the question is whether confidence can be restored in the NFF as it grapples with both sporting disappointments and off-field challenges.