Science education and environmental education are important gates to prepare the next generation for our society’s current and upcoming challenges. While in the informal sector, environmental education acts independently, on the formal side, science education hosts environmental issues within its interdisciplinary context. As both educational efforts traditionally bear different emphases, the question may arise of whether formal science classes can act as an appropriate host. Against the background of the declining motivation to learn science in secondary school, possible synergies between both educational efforts may have vanished. For an investigation of such linkages between science motivation and environmental perception, we monitored adolescents’ motivation to learn sciences and their environmental values. By analyzing data from 429 Irish secondary school students, we reconfirmed existing scales by using confirmatory factor analysis (CFA) and investigated potential relations via SEM. Besides gender differences, we identified a significant relationship between positive ‘green’ attitude sets and the individual motivation to learn science—positive environmental preferences predict a high science motivation, primarily intrinsic motivation. Taking advantage of this relationship, individual motivation may find support from environmental educational initiatives with the focus on green values. Especially girls, who evidentially tend to have a lower motivation in science learning, may be addressed in that way.