Summary: Economic assessment of energy-related processes needs to adapt to the development of large-scale integration of renewable energies into the energy system. Flexible electrochemical processes, such as the electrolysis of water to produce hydrogen, are foreseen as cornerstones to renewable energy systems. These types of technologies require the current methods of energy storage scheduling and capacity planning to incorporate their distinct non-linear characteristics in order to be able to fully assess their economic impact. A combined scheduling and capacity planning model for an innovative, flexible electricity-to-hydrogen-to-ammonia plant is derived in this paper. A heuristic is presented, which is able to translate the depicted, non-convex and mixed-integer problem into a set of convex and continuous non-linear problems. These can be solved with commercially available solvers. The global optimum of the original problem is encircled by the heuristic, and, as the numerical illustration with German electricity market data of 2013 shows, can be narrowed down and approximated very well. The results show, that it is not only meaningfulness, but also feasible to solve a combined scheduling and capacity problem on a convex non-linear basis for this and similar new process concepts. Application to other hydrogen based concepts is straightforward and to other, non-linear chemical processes generally possible.