Nano- and micron-sized catalysts are continuously being discovered as efficient tools for pollutant oxidation. Their small size motivates their entrapment in beads or capsules for easier handling, but this is normally followed by reduced reaction kinetics due to slower mass transfer within the encapsulation matrix. In this study, liquid-core encapsulation was explored as a way to overcome this limitation. Biogenic manganese oxides (BioMnOx) were chosen as representative catalysts of interest, and two organic pollutants, glyphosate and bisphenol A, were used as model substrates. Different capsule compositions were examined to ensure rapid diffusion with high preservation of oxides and the oxide-forming bacteria. Glyphosate oxidation was found to follow the reported behavior of abiotic birnessite and was highly dependent on pH and oxide concentration. Thanks to the strong relationship between oxidation kinetics and oxide levels, the BioMnOx localized inside the capsules removed glyphosate significantly faster than suspended oxides, and their reuse for several treatment cycles was demonstrated. Bisphenol A, which is more sensitive to diffusion rates than to oxide concentrations, was removed by encapsulated BioMnOx at nearly the same speed as in suspension. Such encapsulation allows simple separation and concentration of reactive surfaces and enables fast transport of substrates in and transformation products out of the capsule, making it a promising way to simplify the use of suspended catalysts at improved performance.