Probiotic foods are recognized for their importance on human health. Kefir is a versatile probiotic food that can be made from non-dairy sources for vegan diet. This study evaluated the addition of microalga Haematococcus pluvialis (0.50% w/v) and blueberry Vaccinium myrtillus (0.50% w/v) extracts to compare their influence on the biochemical properties and the bacterial community of coconut milk kefir through Nanopore-based DNA sequencing. Results revealed that the V. myrtillus increased the microbial diversity in coconut milk kefir with more abundant Proteobacteria species such as Lacticaseibacillus paracasei (22%) and Lactococcus lactis (6.3%). Microalga demonstrated the opposite effect on C, making Firmicutes represent the whole of the microbiota. Biochemical analysis revealed increased fat content in the kefir samples, with the C1 registering 1.62% and the 1.07% in C2, in contrast to the control group’s 0.87% fat content. The crude protein content exhibited a decrease in both samples compared to the control group (0.00% and 0.88% versus 1.07%). These findings suggest that fortifying vegan kefir with prebiotics has the potential to induce significant alterations in the kefir microbiota.