In a series of studies we have investigated means to improve the conversion performance and the use of mixed feedstocks in the process, including pretreatment, yeast propagation and co-fermentation of biomass-derived glucose and xylose, and the trade-offs that need to be made. Fermentation design and pre-adaptation of the fermenting microorganism during propagation was investigated with regard to robustness and efficacy in promoting tolerance to inhibitors and xylose utilization during co-fermentation. However, a trade-off exists in pre-adaptation between improving the performance of the microorganism and obtaining high biomass yield in the propagation step. In addition, fermentation design requires various trade-offs to maximize yields. Pretreatment of mixed feedstocks diversifies the feed stock base, but requires a departure from optimal pretreatment conditions for pure feedstock. However, ethanol yields on par with pure feedstocks could be obtained and thus can the sensitivity towards changes in feedstock availability and prices be hedged.