Early self-regulatory abilities are considered key predictors of children’s behavioral problems and academic competence. However, little is known about whether behavioral problems mediate the association between self-regulation and academic competence, after accounting for key child and family characteristics, during the transition from less structured preschool to more structured primary school contexts. Hence, this study investigated whether behavioral problems at age 5—specifically peer relationship problems, hyperactivity, and conduct problems—mediate the relations between self-regulatory abilities at ages 3–4 (phonological working memory, inhibitory control, cognitive flexibility, delay of gratification, and parent-reported effortful control) and academic competence across receptive vocabulary, mathematical, and scientific domains at ages 6–7, while accounting for relevant covariates (e.g., negative affectivity, socio-economic status). The study drew on data from 1,931 children from a large-scale German longitudinal study. Structural equation modeling showed that self-regulatory facets such as phonological working memory and inhibitory control were directly related to later academic competence both overall and across domains, whereas only parent-reported EC was directly related with behavioral problems. Behavioral problems, in turn, were related to overall academic competence and to the domains of receptive vocabulary and mathematics, but not to science. Accordingly, an indirect pathway via behavioral problems emerged only for parent-reported EC in relation to academic competence — overall and in the domains of mathematics and receptive vocabulary. These results underscore the importance of supporting early self-regulatory abilities—particularly effortful control—through targeted interventions that may help reduce behavioral problems and promote academic competence during the transition to formal schooling.