As petroleum fuels are getting higher in price day after day. I is important to search for an alternative fuel as crude oil will not last forever specially in this high economical and industrial progress. In a parallel way engineers and scientists are searching for additives for the current known fuel until they find the best alternative fuel which has to fulfill the pollution and technical requirements. One of the solution is to implement the idea of downsizing engine fuelled with alternative biodiesel - in this case manufactured by the transestrification by using microwave heating. The process needs automation to keep control for manufacturing efficiency and quality of fuel properties. Authors show the automation layout and present equipment of test stand. There is short summary of combustion engine emission tests, too.