The emergence of a more sustainable economy in Europe was accompanied by a range of bio‐based products and technologies. As a prominent example, green genetic engineering opens up multiple options to increase agricultural production, but its public acceptance seems to vary by application area. Risk perception explains consumer acceptance of green genetic engineering, which is a necessary precondition for wider technology adoption. This study investigates risk perceptions for four major sources of risk: health related, environmental, socioeconomic and ethical. Data were collected in a laboratory experiment in Germany, with a total of 439 participants. A between‐subject design was employed. The four experimental treatment groups comprised two policy scenarios, namely one only permitting research and development and the other allowing full commercialization of genetically modified products, and two product end‐uses, bioenergy and food. The study shows significant end‐use differences in both the type of policy scenario and the risk dimension in question. In particular, health risks were generally perceived to be lower for bioenergy than food whenever full commercialization was pursued. Furthermore, full commercialization of genetically modified food prompted higher concerns about personal health, whereas use of crops for bioenergy production was broadly related to higher levels of socioeconomic risk. Finally, although the majority of consumers identified health risks as being most relevant, the consequences for the environment evoked the greatest degree of risk perception. In general, our findings lend support for the notion that the policy regime is the most important determinant for risk perception, followed by the type of risk dimension and level of trust in industry.