A process model is used for analysing the economic tradeoffs involved in the synthesis, design and operation of a typical batch fermentation plant involving batch and semi-continuous operations with the recycle of the otherwise waste stream that results after the recovery of the product of interest from the fermentation broth. This recycle contributes to a more complete substrate consumption, water reuse and reduction of the environmental impact of the process. Process variables are optimized simultaneously with the plant structure by formulating the whole optimization problem as a non linear programme (NLP). The environmental concern about producing large amounts of fermentation broth waste was accounted for by penalizing its production combined with allowing their recycle to the different types of fermenters based on process considerations. Optimal design and operation are pursued, analysing the economic tradeoffs involved in selecting the number and operation mode of biomass grow and metabolite fermenters, sugar substrate blending to each fermenter, recycle of fermentation broth waste, initial and final concentrations of biomass, substrate and metabolite, and the role of idle times in the process. The paper reports some optimal plant structures and figures for process variables not implemented in industrial practices but supported by process analysis arguments, thus suggesting that they may be worth exploring.