This paper analyses the operational and economic viability of Stirling engine-run micro-cogeneration units in single-family houses in Spain. Thermal demands for the reference dwelling, sited in three different and representative climatic zones, are obtained based on heating and domestic hot water requirements. By carrying out dynamic simulations of both the conventional and cogeneration installations, their performances are obtained and compared. Additionally, based on the results obtained in the simulations, economic viability of the Stirling engine-based micro-CHP is evaluated, taking into account Spanish regulation and economic framework, particularly fuel and electricity prices. Finally, a sensibility study is carried out in order to evaluate how economic results of these plants are affected by both variations in fuel and electricity prices as well as in initial investment costs. It is concluded that there is no opportunity for these devices to be feasible in new and retrofitted single-family dwellings sited in any climatic zone of Spain but in the coldest ones, where the micro-CHP plants could become viable if the Stirling engine investment cost decreases. Iker González-Pino and Jon Terés-Zubiaga acknowledge the financial support of the Basque Government, through the Department of Education, Universities and Research’s Personnel Research Training Program. Many thanks also to the Laboratory for the Quality Control in Buildings (LCCE) of the Basque Government.