Biofuel production through polygeneration with heat as one of the by-products implies a possibility forcooperation between transport and district heating sectors by introducing large-scale biofuel production into district heating systems. The cooperation may have effects on both the biofuel production costs and the district heating production costs. This paper is the second part of the study that investigates those effects. The biofuel production costs evaluation, considering heat and electricity as by-products, was performed in the first part of the study. In this second part of the study, an evaluation of how such cooperation would influence the district heating production costs using Stockholm's district heating system as a case study was performed. The plants introduced in the district heating system were chosen depending on the future development of the transport sector. In order to perform sensitivity analyses of different energy market conditions, two energy market scenarios were applied. Despite the higher revenues from the sale of by-products, due to the capital intense investments required, the introduction of large-scale biofuel production into the district heating system does not guarantee economic benefits. Profitability is highly dependent on the types of biofuel production plants and energy market scenarios. The results show that large-scale biogas and ethanol production may lead to a significant reduction in the district heating production costs in both energy market scenarios, especially if support for transportation fuel produced from renewable energy sources is included. If the total biomass capacity of the biofuel production plants introduced into the district heating system is 900 MW, the district heating production costs would be negative and the whole public transport sector and more than 50% of the private cars in the region could be run on the ethanol and biogas produced. The profitability is shown to be lower if the raw biogas that is by-produced in the biofuel production plants is used for combined and power production instead of being sold as transportation fuel; however, this strategy may still result in profitability if the support for transportation fuel produced from renewable energy sources is included. Investments in Fischer-ropsch diesel and dimethyl ether production are competitive to the investments in combined and power production only if high support for transportation fuel produced from renewable energy sources is included.