This study describes the development and implementation of an iterative diagnostic and intervention routine designed to elicit and quantitatively describe aspects of student metacognition, affect, and study habits in a first-year undergraduate biology course. The Student Metacognition, Affect, and Study Habits (SMASH) inventory is a student-centered questionnaire implemented in tandem with summative assessments and an exam wrapper. SMASH differs from published metacognition instruments by serving the dual purposes of both diagnostic tool and intervention designed to promote metacognitive practice through repeatedly and explicitly linking student attitudes and malleable behaviors to a specific course and to course performance. Exploratory factor analysis of responses provided to inventory items from students in a first-year introductory biology course identified four underlying constructs: Systematic Study Habits, Social Learning, Perceived Difficulty, and Help Seeking. Regression models indicated that student responses to items in Perceived Difficulty predict performance in the study population, suggesting that even a single implementation of the SMASH inventory can provide valuable information.