Harmful non-indigenous species (NIS) introductions lead to loss of biodiversity and serious economic impacts. Government agencies have to decide on the allocation of limited resources to manage the risk posed by multiple NIS. Bioeconomic modelling has focused on single species and little is known about the optimal management of multiple NIS using a common budget. A comprehensive bioeconomic model that considers the exclusion, detection and control of multiple NIS spreading by stratified dispersal and presenting Allee effects was developed and applied to manage the simultaneous risk posed by Colorado beetle, the bacterium causing potato ring rot and western corn rootworm in the UK. A genetic algorithm was used to study the optimal management under uncertainty. Optimal control methods were used to interpret and verify the genetic algorithm solutions. The results show that government agencies should allocate less exclusion and more control resources to NIS characterised by Allee effects, low rate of satellite colonies generation and that present low propagule pressure. The prioritisation of NIS representative of potential NIS assemblages increases management efficiency. The adoption of management measures based on the risk analysis of a single NIS might not correspond to the optimal allocation of resources when other NIS share a common limited budget. Comprehensive bioeconomic modelling of multiple NIS where Allee effects and stratified dispersal are considered leads to a more cost-effective allocation of limited resources for the management of NIS invasions.