Milk kefir and water kefir are fermented beverages traditionally produced by inoculating milk or a sugar-rich solution with a symbiotic microbial ecosystem contained within kefir grains. While these beverages have been consumed in certain regions for centuries, their global popularity has surged recently, prompting more research into their microbiomes. Kefirs are also studied as interesting model microbial communities. We applied genome-resolved metagenomic analysis to milk and water kefir metagenomes, derived from the same initial microbial population, to study compositional change and microbial evolution at the species and strain level. Citizen scientists contributed by fermenting kefir using different substrates and growth conditions for up to 21 weeks, starting with a common source of kefir grain. Our findings showed a period of rapid compositional change from weeks one to nine (wk01-wk09) in both milk and water kefir liquid and grain microbiomes. This period was followed by greater stability for many, though not all, metagenomes from weeks 13 to 21 (wk13-wk21). We documented evolutionary changes in several prevalent species, revealing higher mutation rates during the initial weeks compared to later stages. Both milk and water kefir metagenomes frequently contained bacteria not typically associated with kefir communities, likely acquired from the environment. Although no potentially pathogenic species persisted in the kefir grains throughout the 21-week study, some did persist over extended periods. Ultimately, our findings provide new insights into how microbial ecosystems change and evolve over successive fermentations.