Transdisciplinary research (TDR) is conceptualized as not only providing societal effects but also benefiting academia. However, recent literature on the evaluation of TDR has focused almost entirely on the societal effects of TDR. A discussion of the scientific effects of TDR is needed to do justice to the potential of this research mode. To date, little empirical research has focused on the effects of TDR on science. Our explorative study addresses this gap. The empirical basis are qualitative interviews with scientists engaged in transdisciplinary research and anchored in three sub-disciplines: environmental sociology, sustainable chemistry, and participatory health research. We identify as main effects of the transdisciplinary research mode: changes in the understanding of scientific problems, changes in the quality of scientific insights, and the promotion of a reflexive turn in science.