Aloe vera gel is a globally popular natural product used for the treatment of skin conditions attributed to the presence of bioactive polysaccharides. Nearly 25% of circa 500 species in the genus Aloe are used locally in traditional medicine, indicating that the bioactive components in Aloe vera may be common across the genus Aloe. The complexity of the polysaccharides has hindered development of relevant assays for authentication of Aloe products and analysis of the constituent monosaccharides have been proposed but found to be too conservative. Carbohydrate microarray polymer profiling has recently been suggested as a method for profiling Aloe polysaccharide composition. The aim of this study was to use carbohydrate microarray polymer profiling to investigate the seasonal variation in the polysaccharide composition of two medicinal and two non-medicinal Aloe species over the course of a year. Microscopy was used to explore where in the cells the bioactive polysaccharides are present and predict their functional role in the cell wall structure. The CoMPP analyses showed clear differences in the polysaccharide composition between the different species and CoMPP therefore has potential as a complementary screening method directly targeting the presence and composition of relevant polysaccharides. The results also show changes in the polysaccharide composition over the year within the investigated species, which may be of importance for commercial growing in optimizing harvest times to obtain higher yield of relevant polysaccharides.