Affective factors such as the achievement emotions are considered critical for students' academic performance in STEM degree programmes and careers. In this study, a reciprocal causation model was tested between two affective factors: enjoyment and anxiety, and organic chemistry course performance. Each variable was measured three times in four sections of a first semester organic chemistry course. This study investigates a reciprocal causation relationship between anxiety, enjoyment and achievement as measured by exam performance compared to unidirectional structures of performance and affect relationships. Results show that the reciprocal causation model with an exam snowballing effect best fits data among the alternative models. There is a small and significant negative relationship between anxiety and performance contrasted with a positive relationship between enjoyment and performance throughout the semester. The evidence of the reciprocal relationship between anxiety, enjoyment and achievement indicates that instructors of organic chemistry can work to eliminate factors associated with low performance. Gathering information regarding anxiety and enjoyment along with performance can inform educators about the emotional state of their classrooms. Future research should consider achievement emotions in light of educational reforms to ensure that innovative curricula or pedagogies are functioning in the classroom as intended.