Temperature is a key parameter of anaerobic digestion. Its modification can have drastic consequences on microbial communities and performances. However it can be an interesting parameter to adjust the productivity, energy efficiency or stability of bioreactors. The objective of this work was to give insights into the consequences of abrupt temperature modifications on the microbiota of anaerobic digestion. Two complementary experiments were performed. A continuously stirred lab-scale bioreactor (5-L) simulated the functioning of a semi-continuous industrial digester. Five batch-fed incubations (1-L) served as replicated experiments. Each experiment was divided into three successive steps: reactors were first operated at 35 degrees C followed by an abrupt increase to 55 degrees C and finally a decrease to 35 degrees C. After the first temperature shock, gas production rate increased temporarily and then fell for 1 month before a new steady-state was reached. When temperature was reset to 35 degrees C in step 3 gas production decreased sharply again. The semi-continuous reactor recovered after 15 days while the batch-fed incubations never recovered. Ecological changes associated to these performance drops and recovery were sought using 16S sequencing of Bacteria and Archaea and multivariate analyses. In brief, Bacteroidales order was rapidly and strongly affected by temperature increase, while Clostridiales became dominant in thermophilic conditions. Several thermotolerant Bacteria were identified as responsible for reactors early recovery, but were outcompeted by a very diverse bacterial population a few weeks after temperature shock. Methanosarcina and Methanobacterium Archaea dominated at 35 degrees C but were slowly replaced by thermophilic Methanoculleus or Methanosarcina at 55 degrees C that were essential to methane production. In step 3, when returning to initial temperature conditions after the thermophilic period, Ruminococcaceae and Methanobacterium appeared to drive digester resilience.