Decentralized wastewater treatment is a viable and sustainable alternative to having universal access to sanitation, especially for developing countries and small communities. Chlorine and peracetic acid (PAA) have been studied widely to promote wastewater disinfection, however there are few comparative studies applied to decentralized wastewater treatments. This paper investigated the application of chlorine and PAA in two biological reactor effluents regarding disinfection, organic matter oxidation, and odor control. Full factorial design was used to quantify the effect of the Chlorine and PAA dose (5, 10, and 15 mg L-1) and contact time (5, 10, and 15 min) in the batch experiments. Chlorine and PAA were inefficient in reducing the organic matter showing an increment in the chemical oxygen demand (COD) concentration in most of the tests. Sulfide was oxidized by chlorine (0.0-39.9 %) and PAA (3.5-73.5 %) for both reactor effluents. Inactivation results from E. coli and total coliform by chlorine and PAA showed that the effluent quality has a stronger influence than the disinfectant type. The best operational condition (15 mg L-1, 15 min) were also tested in the continuous mode flow, whose results are in agreement with those found in the batch tests. These results provide valuable support in terms of establishing practical guidelines for chlorine and PAA applications in decentralized wastewater treatment in Brazil. (C) 2020 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.