This study explored students’ motivation and difficulties in learning programming in a blended learning environment. The face-to-face classroom instructions were blended with digital learning instructions. The study adopted a convergent parallel design mixed methods research and involved 209 pre-university students. The findings were as follows: (i) Looping was hard. Students faced difficulties in program design, problem-solving, and debugging of repetition structures. (ii) Students with prior programming experience were more motivated to learn by innate psychological needs: autonomy and competence. (iii) Competence motivated students performed better in programming, but no significant findings for autonomy and relatedness motivated students. A blended learning environment must be structured around the nature of the subject to satisfy students’ innate psychological needs. Digital learning materials can support understanding of certain programming concepts, but teaching instructors play an important role in providing academic, mental, and emotional support.