El Chichón is an active volcano located in the Chiapas Volcanic Arc characterized by high temperatures, low pH, and large heavy metal concentrations. High temperatures are known to affect microorganisms, so the bacterial community structure was investigated in crater-lake sediment at a ‘low’ 50 °C and a ‘high’ 92 °C by sequencing the 16S rRNA bacterial gene. Most metal concentrations, and bacterial richness, and diversity indexes were higher at 50 °C than at 92 °C. Fifteen phyla were found in the sediment at 50 °C dominated by Actinobacteria (33.1%), Proteobacteria (29.1%) and Acidobacteria (20.1%). Nine phyla dominated by Firmicutes (52.7%, mostly Alicyclobacillus and Sulfobacillus) and Proteobacteria (44.8%, mostly Bradyrhizobium, Methylobacterium, Sediminibacterium) were detected in the sediment at 92 °C. The predictive functional profiling indicated metabolic pathways related to amino acid metabolism, membrane transport, replication, and repair as the most important. It was found that although a large number of bacterial groups were well adapted to 92 °C, the higher temperature reduced strongly, the bacterial diversity and species richness in the El Chichón volcano crater-lake system, and altered the bacterial community structure and their functionality.