The coronavirus disease 2019 pandemic brought changes to almost every segment of our lives, including dietary habits. We present one among several studies, and the first on the Croatian population, aiming at investigating changes of food choice motives before and during the pandemic. The study was performed in June 2021 as an online-based survey, using a 36-item Food Choice Questionnaire applied for both the periods before and during the pandemic. The final sample consisted of 1232 adults living in Croatia. Sensory appeal was ranked as the number one most important food choice motive before, whereas health was ranked as the number one most important food choice motive during the pandemic. Ethical concern was reported as the least important food choice motive both before and during the pandemic. In women, natural content (p = 0.002), health, convenience, price, weight control, familiarity, and ethical concern (all p < 0.001) became more important during the pandemic, while price (p = 0.009), weight control, familiarity, and ethical concern (all p < 0.001) became more relevant for men. All together, these can be considered favorable changes toward optimal diets and may result in beneficial influences on health and lifestyle. Education strategies and efficiently tackling misinformation are prerequisites for informed food choice, which will ensure long-lasting positive effects of such changes.