Although researchers call for inquiry learning in science, science assessments rarely capture the impact of inquiry instruction. This paper reports on the development and validation of assessments designed to measure middle-school students' progress in gaining integrated understanding of energy while studying an inquiry-oriented curriculum. The assessment development was guided by the knowledge integration framework. Over 2 years of implementation, more than 4,000 students from 4 schools participated in the study, including a cross-sectional and a longitudinal cohort. Results from item response modeling analyses revealed that: (a) the assessments demonstrated satisfactory psychometric properties in terms of reliability and validity; (b) both the cross-sectional and longitudinal cohorts made progress on integrating their understanding energy concepts; and (c) among many factors (e.g. gender, grade, school, and home language) associated with students' science performance, unit implementation was the strongest predictor.