The adsorption process of lapachol and isolapachol sodium salts (LSS and ISS, respectively) on chitosan flakes was investigated. The aim of this work is to analyze the interaction between chitosan flakes and LSS and ISS, bioactive quinones, looking for the enhancement of their stability and for their controlled release. The effects of contact time, quinone concentration, temperature, and ionic strength on the adsorption of LSS and ISS onto chitosan flakes were studied using a batch adsorption technique. The kinetics of adsorption follows the pseudo-second-order model. Isotherm data were analyzed using the Langmuir and Freundlich models. The adsorption process was found to be endothermic for LSS-chitosan and exothermic for ISS-chitosan. The results have shown the importance of the double bond position in the side chain of the quinone. The stability of both quinones was improved after adsorption on chitosan. An increase in ionic strength decreases the amount adsorbed for both quinones around 50 % for LSS and 20 % for ISS. Release studies of LSS and ISS from chitosan were investigated, indicating that the higher desorbed amount was in the buffered medium.