Hydrogen and ammonia are considered crucial carbon-free energy carriers optimally suited for seasonal chemical storage and balancing of the energy system. In this context, longitudinally staged combustion systems represent an attractive technology in power generation for their capability of achieving low NO x emissions while conserving high load and, crucially, fuel flexibility at high thermal efficiency. Such two-stage combustion systems have been successfully implemented for natural gas firing of gas turbines and, more recently, have shown significant potential for clean and efficient hydrogen-firing operation. However, optimal operation with ammonia-based fuel mixtures is yet to be established. In recent works, a novel Rich-Quench-Lean (RQL) operational concept was proposed to burn a fuel-rich mixture of partially decomposed ammonia and air (for equivalence ratios ϕ∼ 1.1− 1.2) in the first stage of a longitudinally staged combustion system. Complete oxidation of the remaining (hydrogen) fuel is theoretically ensured by dilution-air addition downstream of the first stage combustor. However, any operational concept based on these near-stoichiometric combustion conditions, while minimizing undesired prompt NO x and N 2 O formation by ammonia oxidation, can potentially result in significant, and certainly unpractical, thermal load on the first stage combustor liner that needs to be mitigated. In the present study, we exploit a newly developed reactors-network model to efficiently investigate the NO x-emissions performance of a longitudinally staged combustion system fired with natural gas, hydrogen or ammonia. First, the reactors network framework is validated with experimental, computational and other similar reactor network results in the literature. Second, the optimal air distribution within the longitudinally staged combustion system is found for clean (low emissions) and efficient (complete fuel conversion) ammonia-firing operation. Third, the consequences of such “ammonia-optimized” air distribution on flame stabilization and NO x emissions in more conventional natural gas-and hydrogen-firing operation are considered. Finally, an optimal air and fuel distribution is suggested for the longitudinally staged combustion system on the basis that, while still ensuring robust flame stabilization and high turbine inlet temperature, it minimizes NO x emissions for all three fuels considered.