Carboxylic acids produced by acid fermentation have attracted much attention recently as promising chemical feedstock. The feasibility of the acid fermentation as a high-value added bioconversion process depends on the selective separation of carboxylic acids from the bulk solution. The authors synthesized an aminopropyl-functionalized mesoporous silica nanoparticle (MSN) material with the MCM-41 type, parallel channel porous structure via a co-condensation method. The adsorption isotherms were analyzed with an extended Langmuir model using an overloading term. The highest acid adsorption capacity was 3.38 mol kg⁻¹ for 1 : 1 complexation at an amine density of 3.14 mol N kg⁻¹. Positive isosteric heat showed the reaction was exothermic and favored at low temperature. Desorption/regeneration by increasing the pH to 10.5 was completed within 1 min, and the regenerated MSN showed an adsorption capacity equivalent to the original. MSN had a high selectivity for carboxylic acid over ethanol, glucose, and protein. The pseudo-second-order rate constant for acetic acid adsorption on MSN was 0.41 kg mol⁻¹ min, significantly higher than those of an anion exchange resin (0.14 kg mol⁻¹ min) and activated carbon (0.06 kg mol⁻¹ min). We envision that the MSN material could serve as an efficient adsorbent for selective sequestration of biomass-derived carboxylic acids for various applications.