Background: Despite the growing body of research concerning affective relationships between teachers and ethnic minority students, very little is known about student-teacher relationship (STR) quality for religious minority students. Many Islamic schools have a mixed workforce consisting of both Muslim and non-Muslim teachers. This means that the quality of religiously congruent and religiously incongruent STRs can be directly compared. Aims: We investigated whether the quality of the STR experienced by Dutch Islamic school students depended on the religious background of their teacher (Muslim vs. non-Muslim). We also examined the role of teachers' implicitly measured attitudes towards Muslims as a possible explanation for differences in relationship quality. Sample: Participants were 707 students (56.9% female) from 35 classes (Grade 3-6) (M[subscript age] = 10.02 years, SD = 1.25) and their 35 teachers (85.7% female; M[subscript age] = 32.94 years, SD = 6.37). Methods: Students reported on the quality of the relationship with their teacher (closeness, conflict, and negative expectations), and teachers' implicit attitude towards Muslims (vs. non-Muslims) was measured with an Implicit Association Test. Results: Students reported relatively high levels of closeness and low levels of conflict and negative expectations for both Muslim and non-Muslim teachers. Conflict was slightly higher in religiously incongruent STRs, but only when teachers' implicitly measured attitude towards Muslims (vs. non-Muslims) was included in our model. Conclusion: Results of this study indicate that religious incongruence does not play a major role in STR quality in Islamic primary education.