The chapter investigates modelling competency in problem-oriented project work in the interdisciplinary natural science bachelor program (Nat Bach) at Roskilde University, Denmark. The focus is on analyses of students’ project reports within the area of infectious diseases modelled by the standard SIR compartment model and extensions thereof. Within this domain, the students’ modelling competency is analysed with respect to two dimensions in modelling competency. These are the degree of coverage with respect to the modelling process and the technical level of the modelling work and of the use of mathematics (Blomhøj M, Højgaard T, Modelling and applications in mathematics education: The 14th ICMI study. Springer, New York, pp 45–56, 2007). In addition, two types of students’ related reflections are pinpointed and analysed, namely, reflections related to the particular modelling subprocesses (internal reflections) and reflections concerning the role and function of the model and its results in a context of application (external reflections) (Blomhøj M, Kjeldsen TH, Trends in teaching and learning of mathematical modelling. Springer, Dordrecht, 2011). Based on the analyses and experiences with supervising and assessing students’ modelling project in the Nat Bach program, a framework including the two dimensions and the two types of reflections is promoted as a means of characterising progress in students’ mathematical modelling competency in problem-oriented project work.