Alkali treatment of maize bran can break ferulate cross-linking and increase utilization of alkali-solubilized arabinoxylan (AX) by the human gut microbiome. However, it is not known how alkali treatment affects the utilization of AX and other non-digestible carbohydrates (NDC) that remain insoluble after alkali treatment, or how varying degrees of alkali treatment affect NDC fermentation. Therefore, maize bran was treated with alkali ranging from 0 to 1.25 M NaOH, neutralized, and then subjected to in vitro digestion and fermentation using human fecal microbiomes. Increasing alkali concentration progressively increased water solubility of NDC, especially AX, and increased microbial fermentation of water-soluble AX (p < 0.001) during fermentation; however, there was a decrease in fermentation of insoluble AX and NDC (p < 0.001). Across microbiomes, more acetate (p = 0.004) and propionate (p = 0.018), but less butyrate (p < 0.001), were produced as alkali treatment of maize bran increased. Higher alkali treatments increased the abundances of Bifidobacterium (q < 0.001), Bacteroides (q = 0.0015), Faecalibacterium (q < 0.001), and several genera in the Bacilli class (q < 0.001), while decreasing Bilophila (q < 0.001), Butyricicoccus (q < 0.001), and several Lachnospiraceae (q < 0.001). Soluble but not insoluble NDC utilization was improved by extracting residual free phenolic compounds from alkali-treated maize bran (p = 0.005 and p = 0.39, respectively). In conclusion, alkali makes maize bran AX more water soluble and fermentable, but it has a negative impact on insoluble AX and NDC utilization, which reduces butyrate production by the microbiome due to decreases in Butyricicoccus and some Lachnospiraceae.