Recently, integrated STEM projects have been introduced into school curricula in an attempt to increase students' understanding and interest in pursuing STEM subjects in senior high school and university. However, little is known about the classroom emotional climate in STEM classrooms and its effect, along with teacher-student interpersonal relationships, on students' attitudes towards STEM. A validated questionnaire about students' perceptions of the STEM classroom emotional climate and a simplified version of the questionnaire of teacher-student interpersonal relationships were administered to students completing STEM projects (N = 698). Students also completed a questionnaire about their attitudes towards STEM projects and continuation in the STEM pipeline. Structural equation modelling analysis suggested that the classroom emotional climate together with helping/friendly teacher-student interpersonal relationships have positive influences on student attitudes towards STEM. On the other hand, while teacher-student interpersonal relationships that are understanding or directing have a positive influence on the classroom emotional climate, they have negative influences on students' attitudes towards STEM and continuing in the STEM pipeline. There are some significant gender differences in teacher-student relationships that influence attitudes towards STEM. This raises some interesting possibilities about how teachers should manage classrooms that integrate STEM skills to complete projects in order to encourage greater participation in STEM subjects.