Understanding the role of metacognitive judgements in science learning can significantly contribute to the qualification of both teaching and learning processes. We present some of the existing relationships between two important theoretical categories in education: metacognitive judgements and cellular theory learning. The research was conducted with sixth graders from a public school in the city of Pereira, Colombia through a mixed research design. The results show that as the didactic unit was developed, students qualified their explanatory models about the cell and cellular theory. Their arguments were stronger and more coherent, while their metacognitive judgements displayed different levels of confidence, which improved over the course of time.