Boronate affinity materials, as widely used sorbents for the enrichment of cis-diol-containing molecules, have been rapidly developed and increasingly utilized for various applications in recent years. cis-Diol-containing molecules, including saccharides, nucleosides, catecholamines, glycans and glycoproteins/glycopeptides, are major targets in the frontiers of many research areas, such as environmental analysis, the food industry and bioanalysis. As the analysis of these molecules usually suffers from the low abundance of targets and the high abundance of interference, selective enrichment is a fundamental step of sample preparation before analysis. In this review, we survey recent achievements of boronate affinity materials and their applications in sample preparation. We mainly focus on the fundamental considerations of materials as well as important applications in the past 3 years. Particularly, the effects of the substrate structure on the performance of boronate affinity materials, such as binding capacity, affinity, selectivity and working pH, will be discussed. Furthermore, the applications in sample preparation will also be introduced, with a main emphasis on what merits can be provided by boronate affinity materials to overcome the challenges in sample preparation.