Balancing conceptual depth with practical skill development is a persistent challenge in advanced machine learning (ML) education, where powerful frameworks can obscure underlying mathematical and computational principles. To address this, we defined a new principled approach that we call full-stack machine learning (FSML), which emphasizes the construction of large language models and diffusion models from scratch. To evaluate the effectiveness of FSML, we conducted a classroom-based randomized controlled trial (N=208) in which FSML-based instruction was compared against a popular library-based instructional approach. We measured students’ conceptual understanding through a specialized assessment and administered a survey capturing knowledge-gap awareness, curiosity, and cognitive load. We found that students who received FSML instruction performed approximately 10% better than control participants in a quiz on transformers and stable diffusion (p=0.006). They also showed increased curiosity and more positive affective responses, suggesting deeper engagement with ML fundamentals. Our findings indicate that our full-stack approach to ML education can improve student learning outcomes, potentially reshaping curricula for ML and other advanced computing topics.