This paper examines the practical operation of the separation of powers in Nigeria’s presidential system, arguing that constitutional design, political economy factors, and institutional legacies have fostered significant executive dominance. It analyses how control over fiscal resources, patronage networks, and security apparatuses enables the presidency to undermine legislative and judicial autonomy. The study employs a qualitative case study methodology, drawing on documentary analysis of budgetary processes, judicial rulings, and legislative-executive conflicts from 1999 to 2021. The findings reveal a cyclical pattern where economic governance structures centralise power, which in turn weakens accountability and perpetuates a political economy conducive to executive overreach. The discussion situates these dynamics within broader debates on democratic consolidation and institutional resilience in African presidential regimes.