Away from on-field results, the NFF is under scrutiny for its governance and financial stewardship.
Much of the focus is on a 17bn naira ($12.66m, £9.31m) intervention package reportedly approved by President Bola Tinubu in 2024 to clear arrears and other obligations owed to the national teams.
Although no official conclusions have been released, sources familiar with the matter say the ongoing review is examining financial records and administrative practices.
Separately, an NFF fact-finding panel formed after Nigeria’s Wafcon 2026 exit flagged multiple issues at board level and in the management of the national teams.
Its report alleged that board members have influenced squad selection and that some officials and even coaches have prioritized financial gain over merit in player call-ups.
The upcoming emergency congress is expected to address the status of the executive committee and compliance with the statutes of the NFF, the Confederation of African Football, and FIFA.
This uncertainty casts doubt on NFF elections planned for September, with a FIFA-backed normalisation committee being discussed as a possible interim measure to oversee a transition and prepare for new polls.
Calls for far-reaching reforms have intensified in recent months.
Former Nigeria internationals, including John Obi Mikel, Jay-Jay Okocha and Segun Odegbami, argue that genuine progress requires breaking with long-standing administrators associated with years of underperformance.
While the resignations add to the instability, some stakeholders see an opening for overdue structural changes and a cultural reset.
This upheaval is unfolding amid wider global debates about governance and accountability in football, with FIFA boss Gianni Infantino central to the discussion.
For Nigeria, the central question is whether trust can be restored in the NFF as it tackles both on-field setbacks and off-field challenges.