This study examines the effects of COVID-19-related measures on the mathematics achievement of university students in social sciences in Slovenia. Our particular concern was to compare two student populations (pre-pandemic and pandemic) in terms of factors affecting student performance in mathematics courses. Data were collected over nine consecutive academic years (from 2013–2014 to 2020–2021) and analyzed using two-stage structural equation modelling (SEM). The analyses confirmed that the conceptual model developed before the pandemic was applicable during the pandemic period. For both populations (pre-pandemic and pandemic), mathematics confidence, perceived level of math anxiety, background knowledge from secondary school, and self-engagement in mathematics courses at university were confirmed as factors influencing mathematics achievement. Moreover, both populations perceived the effects of the factors in the same way, and the magnitude of the effects is comparable. The rather high values of determination coefficient for mathematics achievement (greater than 0.66 for both student populations) indicate that the variables “Perceived Level of Math Anxiety” and “Self-Engagement in Mathematics Course at University” together explain a significant proportion of the total variance before and during the pandemic. Consequently, the results of our case study indicated that pandemic measures did not have a significant impact on our students’ mathematics achievement. Although a more in-depth study of a broader sample of academic courses would be needed to confirm our findings, our experience indicates that mathematics courses at the tertiary level of education can be successfully delivered online.