The ecological modernisation of enterprises has led to significant levels of total emissions in the atmosphere. This is a very important and complex issue for the Republic of Armenia (RA). An agent-based model was developed to determine the best trade-offs for the ecological modernisation of enterprises. The aim is to solve the bi-objective optimisation problem, the objectives of which are the ‘Integrated Volume of Total Emissions’ and the ‘Integrated Index of Industrial Production’. The results indicate that it is possible to reduce the total emissions in the atmosphere by more than 20% for a ten-year period. This may be done by keeping up the positive dynamics of industrial production through choosing trade-offs in the frame of the ‘Pareto-optimal ecological modernisation’ scenario. The scenario was obtained with the help of the suggested genetic algorithm, modified for the problem of the binary control of transitions from initial non-ecological states of each enterprise, towards the target state of ecologically pure manufacturing.