Sewage sludge from sewage treatment plants has soil-forming and fertilising properties. However, sewage sludge cannot always be used in nature, including agriculture. One of the main reasons is the concentration of heavy metals. Sludge from wastewater treatment plants operating in MBR (membrane biological reactor) and SBR (sequential batch reactor) systems was analysed. Studies comparing the risk analysis of the natural use of sludge from MBR and SBR treatment plants were performed for the first time, due to the fact that more and more MBR plants, which are a BAT technology, are being developed in Poland, displacing the classical SBR plants. MBR technology uses a combination of activated sludge and filtration with microfiltration membranes. Wastewater treated in these reactors meets the highest quality standards, both in terms of physicochemical and microbiological aspects. This paper presents studies on the mobility of heavy metals in sewage sludge carried out using the BCR sequential extraction method. Geo-accumulation index (GAI), potential environmental risk index (ER), risk assessment code (RAC), and environmental risk determinant (ERD) were calculated. Heavy metals dominated the stable fractions in all cases. Furthermore, an increased content of copper and cadmium was observed in the MBR sludge. This fact is favourable in view of the efforts to eliminate heavy metals in the environment.