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Algorithmic bias in educational environments has garnered increasing scrutiny, with numerous studies highlighting its significant impacts. This research contributes to the field by investigating algorithmic biases, i.e., selection, label, and data biases in the assessment of students’ affective states through video analysis in two educational settings: (1) an open-ended science learning environment and (2) an embodied learning context, involving 41 and 12 students, respectively. Utilizing the advanced High-speed emotion recognition library (HSEmotion) and Multi-task Cascaded Convolutional Networks (MTCNN), and contrasting these with the commercially available iMotions platform, our study delves into biases in these systems. We incorporate real student data to better represent classroom demographics. Our findings not only corroborate the existence of algorithmic bias in detecting student emotions but also highlight successful bias mitigation strategies. The research advances the development of equitable educational technologies and supports the emotional well-being of students by demonstrating that targeted interventions can effectively diminish biases.