Abstract This paper assesses unintentional interference between different public policies promoting energy efficiency and renewable energy. The paper develops a methodology to study the interference by analysing the economic and technical behaviour of a hybrid energy system. The hybrid energy system in this case consists of an existing cogeneration unit extended with a new installation of thermal solar panels. This puts two complementary heating technologies in juxtaposition. The two technologies are supported with distinct regional support instruments in each region. The design and operation of the energy system is optimised from the point of view of the investor according to the different support instruments. The optimal configuration is analysed as well as its effect on reduced CO 2 -emissions during the lifetime of the project. The methodology is applied to a case-study for two neighbouring regions, the Netherlands and Flanders. The policies in the Netherlands show a beneficial synergy. In Flanders, the hybrid energy system is not interesting, indicating unbalanced high support for cogeneration in this case. From the point of view of the authorities, a more balanced regional policy as in the Netherlands provides a larger CO 2 -emission reduction for a smaller cost.