Recovery from stress is an important property for anaerobic digestion (AD). Although AD is quite adaptable with regard to waste composition, new substrates added to stable systems may cause process decline. We tested whether crude glycerol would cause stress to a thermophilic AD microbiome previously stabilized long-term on a low C/N ratio feedstock. Three-percent (v/v) crude glycerol was added to the basal substrate (poultry litter) for two hydraulic retention time (HRT) periods. This caused stress where biogas volume and methane percentage dramatically decreased and VFA levels increased. When the basal substrate was resumed, secondary inhibition occurred, resulting in even greater stress (biogas production ceased, methane 3.6%). Unassisted recovery of system processes required eight HRT periods. In contrast, crude glycerol applied at a lower organic loading rate did not cause inhibition. Crude glycerol caused changes in dominance in the microbial community (16S rRNA pyrotags). Although process resilience was slow, the recovery of digester functions occurred in conjunction with the recovery of community structure, particularly putative syntrophic acetate-oxidizing bacteria.