This study aimed to examine whether mathematics learning motivation and negative academic emotions differ simultaneously according to grade level, age, and gender among elementary school students. A quantitative cross-sectional comparative survey design was employed involving 260 students in Grades 3–5 from elementary schools in Cirebon Regency, Indonesia, selected through purposive sampling. Data were collected using two self-report questionnaires measuring mathematics learning motivation and negative academic emotions on five-point Likert scales. Instrument measurement properties were evaluated using SmartPLS 3, while descriptive statistics and Multivariate Analysis of Variance (MANOVA) were performed using IBM SPSS, with Pillai’s Trace used as the principal multivariate statistic. The findings revealed significant multivariate differences in the combined outcomes according to grade level (p < .001) and age (p = .015), whereas gender differences were not significant (p = .474). Follow-up analyses showed that these differences were attributable primarily to negative academic emotions, which differed significantly across grade levels (p < .001) and age groups (p = .003), while mathematics learning motivation remained relatively stable. Neither motivation nor negative academic emotions differed significantly by gender. The study concludes that negative academic emotional experiences were more differentiated by grade level and age than overall mathematics learning motivation. The study contributes multivariate evidence from the Indonesian elementary education context by examining motivation and negative academic emotions concurrently, highlighting the relevance of students’ emotional experiences alongside motivation in mathematics learning.