We investigated students' conceptual learning of energy topics in an innovative college-level introductory mechanics course, entitled Matter & Interactions (M&I) Modern Mechanics. This course differs from traditional curricula in that it emphasizes application of a small number of fundamental principles across various scales, involving microscopic atoms, macroscopic deformable objects, and large-scale planetary systems. To best match the unique features of this course, a multiple-choice energy assessment was developed. We followed the development framework and explicitly delineated test purpose, scope, and specifications to guide the design, implementation and evaluation of the energy assessment. Also, particular attention was given to: (1) categorizing content and cognition levels and (2) determining reasoning steps of each test item--aspects that often were not explicitly addressed in designing prior concept assessments. We implemented the energy assessment as a written test before and after course instruction with M&I students at two research universities. Interviews were also conducted to explore students' reasoning in applying energy concepts. Results showed that positive change in student conceptual understanding after course instruction was significant on the entire assessment, on individual items, and on individual test objectives. Subsequent interviews further revealed that after instruction students could properly apply the Energy Principle and perform qualitative analysis without using formula sheets. However, students still showed difficulty in dealing with systems involving deformable objects. This study exemplifies practical means of establishing and evaluating key assessment features, provides evidence for the effectiveness of a principle-focused approach to physics learning, and offers useful implications for teaching energy topics.