Abstract Whether scientific reasoning is a domain‐general or domain‐specific ability remains controversial. This longitudinal study followed 53 German aged 6–9 years (31 females, 22 males) from kindergarten into elementary school to investigate how kindergarten‐age scientific reasoning, intelligence, and disciplinary knowledge influence their third‐grade mathematics and German language abilities (based on teacher ratings). Scientific reasoning was assessed with comprehensive inventories (the Science‐Kindergarten and the Science‐Primary School Reasoning Inventories). Intelligence, language abilities (receptive language and text comprehension in kindergarten and elementary school, respectively), and kindergarten mathematics were assessed with standardized instruments. Kindergarten scientific reasoning predicted third‐grade mathematics abilities independent of parental education levels, and also the intelligence and kindergarten mathematics ability of the children. The language ability of children was predicted solely by kindergarten language abilities. These findings support the view that scientific reasoning is a domain‐general science skill, which is different from intelligence and relevant for mathematics learning among elementary school students.