The recycling of biomass is the cornerstone of sustainable development in the bioeconomy. In this context, digestates and composts from processed agricultural residues and biomasses are returned to the soil. Whether or not the presence of pathogenic microorganisms in these processed biomasses isa threat to the sustainability of the current on-farm prac-tices is still the subject of debate. In this review, we describe the microbial pathogens that may be present in digestates and composts. We then provide an overview of the current European regulation designed to mitigate health hazards linked to the use of organic fertilisers and soil improvers produced from farm biomasses and residues. Finally, we dis-cuss the many factors that underlie the fate of microbial pathogens in the field. We argue that incorporating land char-acteristics in the management of safety issues connected with the spreading of organic fertilisers and soil improvers can improve the sustainability of biomass recycling.