In this study the effects of different learning environments on the promotion of decision-making competence for the socioscientific issue of genetically modified crops is investigated. The comparison focuses on direct vs. indirect instructions. Therefore on the one hand a sophisticated decision-making strategy was presented to the directly instructed experimental group (1) and had to be applied correctly. On the other hand indirectly instructed students had to invent an appropriate strategy by themselves (2) based on the given information and the structure of the problem context. Group discussions are analysed qualitatively in order (1) to outline how the given strategy was understood and its results were reflected on by the students and (2) to explore the characteristics of invented strategies and their degree of complexity. Results indicate that the direct instruction of complex decision-making strategies may lead to a lack of understanding of the decision process when the given strategy is applied and therefore may cause rejection of the final decision. Indirectly instructed students were able to invent sophisticated decision-making strategies containing compensatory trade-offs. It is concluded that when directly instructing complex decision-making strategies, essential parts of reflection have to be integrated in order to gain greater transparency. Accordingly, empirical evidence has been found to consider indirect instruction as a possible way to foster decision-making strategies for complex socioscientific issues even if compensatory procedures are considered to be necessary.