Cryoconite holes are small depressions of the glacier surface filled with melting water and with a wind-blown debris on the bottom. These environments are considered hot spots of biodiversity and biological activities on glaciers and host communities dominated by bacteria. Most of the studies on cryoconite holes assume that their communities are stable. However, evidence of seasonal variation in cryoconite hole ecological communities exists. We investigated the variation of the bacterial communities of cryoconite holes of Forni Glacier (Central Italian Alps) during the melting seasons (July–September) 2013 and 2016, for which samples at three and five time-points, respectively were available. Bacterial communities were characterized by high-throughput Illumina sequencing of the hypervariable V5−V6 regions of 16S rRNA gene, while meteorological data were obtained by an automatic weather station. We found consistent trends in bacterial communities, which shifted from cyanobacteria-dominated communities in July to communities dominated by heterotrophic orders in late August and September. Temperature seems also to affect seasonal dynamics of communities. We also compared bacterial communities at the beginning of the melting season across 4 years (2012, 2013, 2015 and 2016) and found significant year-to-year variability. Cryoconite hole communities on temperate glaciers are therefore not temporally stable.