Methods are provided for controlling metabolic flux rate in a cell-free system comprising a complex set of enzymes, to produce a desired product of a pathway of interest. In the methods of the invention, measurements of metabolic performance parameters are taken by continuous monitoring or intermittent monitoring. Based on the metabolic performance parameters, the system is modified by one or more steps comprising: (i) altering enzyme levels in the cell-free system; (ii) altering feed rate of a substrate that controls redox flux or carbon flux to the cell-free system; (iii) altering 02 addition to the cell-free system; (iv) controlling efficiency of electron transport system by altering leakage across a membrane; wherein enzymes present in the pathway of interest catalyze production of a desired product.