This study aims to assess the microbial, nutritional, volatile, and sensory characteristics of rice, almond, and chickpea water kefir beverages during refrigerated storage. Plant-based kefirs contained significant amounts of lactic acid bacteria and yeasts. The microbial content of kefirs was stable during 14-day refrigerated storage. Lactic acid, acetic acid, and tartaric acid are commonly detected organic acids in kefir samples. Almond and chickpea kefirs were rich in potassium mineral. Almond kefir had the highest ethanol content among plant-based kefirs, followed by chickpea and rice-based kefirs. Ethyl acetate, acetic acid, propionic acid, hexanoic acid, and benzenemethanol were identified as key volatile compounds in almond kefir and chickpea kefir samples using a GC–MS detector during water kefir fermentation. According to sensory analysis results, significant differences are present for all test parameters except odor. Almond kefir was the most accepted, while the other two kefir samples were below the general acceptance level (P < 0.05).