The advantages and challenges of interdisciplinary science teaching and the respective qualification of teachers are an ongoing topic of discussion, especially in countries with no or only partly interdisciplinary science teaching in secondary education. For example, German secondary science teacher education is almost exclusively discipline-specific. Up to now, research does not focus on the effect of German teacher education qualifying for interdisciplinary science teaching in secondary education from a longitudinal perspective. Thus, we were interested in the influence of current German science teacher education over time: Do (prospective) teachers believe they are capable of interdisciplinary science teaching (i.e., self-efficacy beliefs)? How do their beliefs develop during teacher education? Which advantages and challenges do they perceive regarding interdisciplinary science teaching? Do their perceptions change over time? We surveyed 271 (prospective) biology, chemistry, and physics teachers in 2019, 2020, and 2021. Examining the absolute stability (i.e., the change in the mean) of the self-efficacy beliefs showed no significant changes. Analyzing the relative stability (i.e., the change in the rank order) of the self-efficacy beliefs showed middle and positive correlations between the measurements of neighboring time points. The prospective teachers agreed in majority (>50%) with nine out of seventeen advantages and seven out of seventeen challenges of interdisciplinary science teaching. Three advantages reached over 70% approval: Cross-linking content, Addressing key problems, and Promoting interest in science. Four challenges reached over 70% approval: Lack of teacher education, Out-of-field teaching, Lack of depth in content, and Low motivation of teachers due to low affinity to and education in the subject. Neither do the perceptions change strongly between the time points (absolute and relative stability) nor are they very stable. Moreover, it seems that the (prospective) teachers realize the complexity of interdisciplinary science teaching, e.g., regarding experimentation or missing material, with progressing teacher education. The results, rather including no positive effect of two years of teacher education on self-efficacy beliefs, reveal obstacles for teacher education as well as starting points to support (prospective) teachers regarding interdisciplinary science teaching.