A method of deactivating biomass is set forth. The method includes two stages, a disrupting stage and a rupture stage. The disrupting stage includes the steps of injecting an oxidizer gas into the biomass with minimal or significant elevated pressure and then a depressurizing of the biomass. The steps cause a disruption of cellular membranes of cells present in the biomass. The rupture stage includes the step of injecting the biomass with a rupture gas sufficient to pressurize the biomass to a second elevated pressure following by the depressurizing of the biomass. The injecting and depressurizing steps of the rupture stage can be repeated at least two times in order to rupture the cell membranes and expose residual cell contents.