Invasive plant species threaten native species and habitats causing ecologic, economic and social burden. When creating climate friendly solutions by utilizing plant biomasses in biogas and fertilizer production, safety should be ensured concerning the use of residues. This study concentrates on the treatment of biomasses containing invasive plant material by tunnel and windrow composting, and by farm-scale and laboratory-scale anaerobic digestion (AD) in mesophilic conditions. Germination of the nationally settled and harmful invasive species Lupinus polyphyllus Lindl. was investigated after these processes. In addition, the role of the conditions found in the processes that destroyed seeds were studied, such as the time of exposure, temperature and static pressure. Dormant seeds are well protected against harsh conditions and can survive through various stress factors, but also become vulnerable as more factors are combined and time of exposure is extended. Our results suggest that the risks involved for the utilization of harmful invasive species increase with mesophilic temperatures and single treatments if the processing conditions are not stabile. One-month treatment with windrow composting showed a high risk for dormant seeds of L. polyphyllus seeds to survive, whereby extending the processing time reduced it substantially. Hard coated seeds can thus be broken with a combination of thermophilic temperatures, moisture and static pressure.