This paper discusses the operation of an ammonia reactor for a Power-to-Ammonia (P2A) plant. We develop a dynamic model for an ammonia reactor system consisting of a three-bed quench cooled adiabatic reactor and a feed-effluent heat exchanger. The reactor bed model is formulated as a differential algebraic equations (DAE) system. We use the thermodynamic software Thermolib for rigorous modelling of the thermodynamic functions in the high pressure ammonia reactor. We present a case study of an ammonia synthesis loop in a P2A plant connected to a 250 MW renewable energy source with a capacity factor of 0.4. Static optimisation and stability analysis are performed for the reactor system, which located the optimal operating point close to instability. The dynamic simulations confirm the unstable operating regions as severe oscillations arise. A fluctuating energy supply from renewable sources requires the ammonia reactor to operate over a wide operating window from 20%–120% of nominal capacity. We formulate a realistic strategy for varying the supply of H2 and N2 (load) to the synthesis loop depending on the available energy. Open-loop simulations show that varying the synthesis feed flow cause oscillations in the ammonia reactor system. Therefore, we propose a regulatory control structure for stabilising the ammonia reactor. The optimisation algorithm determines the reactor set-point state by updating at changes to the synthesis loop load. Hereby, we achieved fast control and close tracking of the set-points for the ammonia reactor.