Methods and systems are disclosed that monitor the carbon and hydrogen production of a pyrolysis reactor system and adjust one or more inputs to the reactor system to improve performance when one or both of the monitored carbon and hydrogen production falls outside of a target performance specification. In particular, the ratio of fuel to oxidant (“fuel/oxidant ratio”) supplied to a combustion chamber of the reactor system is adjusted to below a fuel/oxidant equivalence ratio range, defined as 0.9-1.1, when both carbon and hydrogen production falls below a target carbon and hydrogen specification, and adjusted above the fuel/oxidant equivalence ratio range when only the carbon production falls below a target carbon specification. The target specification can include a number of parameters including production rate, morphology (of carbon), and operating temperature.