Rainfall and geology of the catchment exert a dominant control on the trophic state of endorheic basins. River inflows and runoff provide nutrients, influencing primary productivity in the water column. Through time, paleoenvironmental conditions are recorded as variations within the sedimentary organic fraction. Thereafter, microbial populations settle and develop within sediments and lead to degradation processes as long as they remain active. However, their presence is generally not considered in Quaternary studies. The present study is based on the sedimentary record of the maar lake of Laguna Potrok Aike, southern Patagonia. We investigate the relationship between paleoenvironmental conditions and colonization of the corresponding sediments by microbes. Microbiological and geochemical analyses were combined to determine factors allowing microbes to sustain their activity over time. The study of Holocene sediments, containing dense and active microbial communities, provided means to evaluate the potential of microbial communities as agents of early diagenesis. We show that phosphorus released during organic matter degradation is essential for microbial growth. In highly colonized sediments, microbial communities appear capable of recycling the excreted ammonium, thus accounting for nitrogen fractionation toward high values in bulk sediment. Microbial activity in Laguna Potrok Aike still persists in 30 ka old sediments. Thus, we proposed that future lacustrine studies should include some microbial indicators to assess their impact in diagenetic processes.