(1) Background: This study examines the role of subjective anxiety (mathematics and spatial anxiety), along with physiological responses, in mathematics or math and mental rotation performance in 131 German primary school students (65 girls, 66 boys; Mean age = 8.73 years). (2) Method: Students' preference for math vs. German and their subjective anxiety were assessed using standardized questionnaires. Emotional reactivity was measured using the Galvanic Skin Response (GSR). Math performance was evaluated via percentage scored and completion times on number line estimation, word problems, and missing terms tasks. Spatial skills were assessed using a novel mental rotation task (nMRT) incorporating gender-congruent and -neutral stimuli. (3) Results: Girls outperformed boys on percentage scored on the math task but took longer to complete this. No gender differences were found in performance on the nMRT. Girls demonstrated higher math anxiety and were less likely to prefer math over German. Math anxiety predicted math scores and accuracy on the nMRT while gender predicted math performance and mental rotation response time. Subject preference was associated with longer completion times and emotional reactivity with longer response times. Girls' preference for math and lower emotional reactivity was linked to shorter completion times, while lower math anxiety predicted higher scores. In contrast, these factors did not affect boys' math performance. Additionally, subjective anxiety, emotional reactivity, or subject preference did not impact spatial performance for either gender. (4) Conclusions: Supporting mathematical self-efficacy and emotional regulation, especially in girls, is crucial for enhancing STEM outcomes in primary education. Gender-fair assessment in mental rotation reveals equitable spatial performance and reduces the impact of anxiety.