This study aimed at investigating the issue of domain specificity of motivation across specific science disciplines (chemistry and physics) in combination with influencing factors related with students' academic major and gender. A clustered sampling was used to select 281 participants who were undergraduate students (105 males and 176 females) attending three different academic majors (Environmental Technology, Conservation of Cultural Heritage, Food Technology) at a Greek tertiary education institution. Motivation to learn chemistry and physics was evaluated concurrently using the discipline-specific (Chemistry and Physics) versions of Science Motivation Questionnaire II (SMQ II) denoted as CMQ II and PMQ II, respectively. Discipline-based comparisons showed the existence of domain specificity in motivation with the whole student sample displaying higher motivation to learn chemistry relative to physics in all five motivational scales of SMQ II (self-efficacy, self-determination, intrinsic motivation, career motivation and grade motivation). Multivariate analysis of variance (MANOVA) and discriminant function analysis showed that students' motivation to learn chemistry and physics depends strongly on their academic major. Furthermore, MANOVA provided evidence for a small gender effect on motivation for either chemistry or physics learning. The implications of the current study for effective tailor-made educational practice and research across different science disciplines are critically discussed.