The mental health crisis in graduate education combined with low treatment rates among engineering graduate students underscores the need for engineering graduate programs to provide effective methods to promote well-being. There is an extensive body of neuroscience research showing that contemplative practices, such as mindfulness, produce measurable effects on brain function and overall well-being. We hypothesized that a mindfulness-based training program designed for engineering graduate students would improve emotional well-being and, secondarily, enhance research capacity. An initial pilot study was conducted at a single institution (Phase 1), followed by a larger study conducted at both the original and a second institution (Phase 2) to gather additional data and show the program’s transferability. The program comprised eight weekly mindfulness training sessions. Individuals in the study were randomly assigned to either an intervention group or wait-list control group. We administered pre- and post-test surveys with quantitative measures designed to assess emotional and physical well-being, as well as creativity, research satisfaction, and desire to contribute to the betterment of society. Participants also completed a summative survey to evaluate the impact of the program on their well-being and research. Analysis revealed statistically significant findings: improved emotional health, decreased neuroticism, increased positive affect, decreased negative affect, and increased mindfulness in the intervention groups compared to the control groups. Intervention groups in Phase 2 also reported statistically significant improvement in satisfaction with their research. Our findings suggest that mindfulness training has the potential to play a vital professional and personal development role in graduate engineering education.