In 2011, EFSA assessed the risk posed by the possible use of dead‐in‐shell chicks for the production of processed pet food. In 2014, the European Commission asked for an update on the risk posed by the same material but as raw material for the production of biogas and compost according to standard transformation parameters normally used for Category 3 material. According to current European Union legislation, the following processing method was considered: maximum particle size before entering the processing unit: 12 mm; minimum temperature in all material in the unit: 70°C; and minimum time in the unit without interruption: 60 minutes. A list of pathogens potentially present in the material to be treated was compiled and available literature data were used to assess the ability of the processing methods to inactivate the most resistant pathogens identified. Spores of Clostridium botulinum were identified as the most resistant hazard potentially present in the material to be processed. Circovirus and parvovirus and Enterococcus faecium were considered the most heat‐resistant viruses and non‐sporulating bacterium, respectively. Moreover, depending on storage conditions, the formation of bacterial toxins is possible. The processing methods considered were therefore assessed for their ability to inactivate those hazards. The probability of survival of pathogens related to the use of dead‐in‐shell chicks subjected to the treatment process was considered to be extremely low for the heat‐sensitive pathogens that could be present in the material, which include bacteria such as Salmonella and avian influenza virus. However, this treatment is unable to sufficiently inactivate other relevant hazards (e.g. bacterial spores, thermoresistant viruses and certain bacterial toxins).