To improve the lignocellulose conversion for ABE in high solids fermentation, this study explored the feasibility of cycling the process through the cellulolytic or/and solventogenic phases via intermittent flushing of the fermentation media. Five different flushing strategies (varying medium ingredients, inoculum supplement and cycling through phases) were investigated. Flushing regularly throughout the cellulolytic phase is necessary because re-incubation at 65 °C significantly improved glucose availability by at least 6-fold. The solvents accumulation was increased by 4-fold using corn stover (3-fold using miscanthus) over that produced by flushing only through the solventogenic phase. In addition, cycling process was simplified by re-incubating the flushed cellulolytic phase with no re-inoculation because the initial inoculum of Clostridiumthermocellum remained viable throughout sequential co-culture. This study served as the first proof of the cycling flush system applied in co-cultural SSC and the knowledge gained can be used to design a farm-scale flushing system.