In this study, chemical oxidation was applied to treat three contaminated sediments. All the sediments were contaminated with mineral oil, polycyclic aromatic hydrocarbons and heavy metals and had an organic matter content ranging from 2.4 to 7.6 %. The natural oxidant demand of the sediments was determined during treatment with two different types of oxidants (potassium permanganate and sodium persulfate), and the effect of these oxidants on the heavy metal release and on the microbial community was investigated. The natural oxidant demands of the sediments under persulfate treatment were lower (30–100 g kg−1) than the ones treated with permanganate (50–450 g kg−1). Cr was released during the application of permanganate whereas Zn and Pb were released under persulfate treatment. qPCR results showed that permanganate and persulfate, both at a concentration of 150 g kg−1, caused a decrease (2 log units) in the number of 16S rRNA gene of total bacteria in the sediment having the lowest organic matter content. However, the total ATP, considered as a biomarker for microbial activity, was below detection limit in all sediments in the presence of at least 150 g kg−1 oxidant. Only permanganate induced a shift in the structure of the microbial community.