During the summer melt season, glacier ice algal blooms are widespread in the area termed “dark zone” in the southwest region of Greenland. Due to their pigmentation, glacier ice algae reduce the albedo of the ice sheet, increasing surface melting. Despite their crucial role in the Greenland Ice Sheet (GrIS) ecosystem, we know little about their metabolic potential or functions. Here, we present insights into the links between microbial community composition using 18S and ITS2 sequencing and total metabolic profiling of samples dominated by glacier ice algae from the GrIS. Our analysis of ITS2 secondary structures reveals that blooms are dominated by a single algal species, yet glacier ice algal haplotype composition differs between sites (along a 40 km transect) and surface habitats (clean snow vs. high algal biomass ice). Furthermore, metabolic composition changes during the development of glacier ice algal blooms with an accumulation of fatty acids, although few differences were observed between sites along the transect. In addition, a few metabolites showed diurnal variations and our data suggest that under low light and freezing conditions, chlorophyll degradation, tocopherol abundance and phytol remobilization may be the key compounds changing in the glacier ice algae dominated samples. Overall, these results improve our understanding of the chemical environment in the GrIS supraglacial microbial community structure and the contribution of the primary producers dominated by the glacier ice algae. Our data also show that endo- and exo-metabolic patterns need to be differentiated and that multiplexed data sets will help gain a better insight into these complex algae- controlled ecosystems.