Conventional techniques to remove Fe impurities in kaolin typically involve high environmental impact and cost. Alternative methods have been focused on the use of bioleaching where Fe in kaolin is reduced with microorganisms. Early results established a noticeable effect of the bacteria on the redox state of Fe, but knowledge gaps persist such as details on the bacterial-kaolin interactions during attachment of bacteria onto kaolin surface, the metabolites produced by bacteria, and changes in Fe(II)/Fe(III) ion equilibria in solution. To bridge these gaps, this study was conducted to determine the detailed physicochemical changes in bacteria and kaolin during bioleaching through surface, structural, and chemical analysis. Bioleaching experiments were conducted for 10 days where each of the three Bacillus sp. was put in contact (at 9 × 108 CFU) with 20 g of kaolin powder using 200 mL of 10 g/L glucose solution. All samples treated with bacteria showed increasing trends in Fe(III) reduction up until day 6 or 8 followed by a slight decrease towards the end of the ten-day period. Examination of scanning electron microscope (SEM) images suggests that bacterial activity damaged the edges of kaolin particles during bioleaching. Ion chromatography (IC) results showed that during bioleaching, Bacillus sp. produced organic acids such as lactic acid, formic acid, malic acid, acetic acid, and succinic acid. EDS analysis of kaolin before and after bioleaching showed Fe removal efficiencies of up to 65.3%. Analyses of color properties of kaolin before and after bioleaching showed an improvement in whiteness index of up to 13.6%. KEY POINTS: • Dissolution of iron oxides by Bacillus species proven with phenanthroline analysis. • Organic acid type and concentration unique to species detected during bioleaching. • Whiteness index of kaolin is improved after bioleaching.