For the choices of food products, food preferences are crucial, as they influence the intake of nutrients and the resultant quality of diet, but in Poland, no studies of food preferences were conducted during the COVID-19 pandemic on a population of young adolescents. The aim of this study was to analyze the determinants of food preferences in a Polish population-based sample of primary school adolescents as part of the Diet and Activity of Youth during COVID-19 (DAY-19) Study. The DAY-19 Study focused on a national sample of a population of primary school adolescents who were recruited based on cluster sampling of participants from counties and schools, yielding a sample of 5039 individuals. Their food preferences were assessed using the Food Preference Questionnaire (FPQ), and they were compared in subgroups stratified by (1) gender: male and female; (2) age: younger (10–13 years) and older (14–16 years); (3) place of residence: urban and rural; (4) Body Mass Index (BMI): underweight, normal body weight, and overweight/obese (assessed based on Polish growth reference values); and (5) physical activity level: low and moderate (assessed using the International Physical Activity Questionnaire for children aged 10–13 (IPAQ-C) and adolescents aged 14–16 (IPAQ-A)). In the population of adolescents, no statistically significant differences in food preferences between subgroups stratified by gender were observed (p> 0.05). For boys, none of the studied factors (age, place of residence, BMI, physical activity level) was statistically significant determinant of food preferences (p< 0.05), while for girls, all of them were statistically significant determinants (p> 0.05). All the assessed factors (age, place of residence, BMI, physical activity level) in girls were associated with preferences for snacks, and older girls, those from a rural environment, those who were underweight and overweight/obese, as well as those having a low physical activity level declared a higher preference for snacks than younger ones (p= 0.0429), those from an urban environment (p= 0.0484), those of a normal body weight (p= 0.0091), and those having a moderate physical activity level (p= 0.0083). Similarly, girls from rural environments declared a higher preference for starches than those from urban environments (p= 0.0103), and girls having a low physical activity level declared a higher preference for fruit than those having a moderate physical activity level (p= 0.0376). Taking this into account, the population of girls, in particular, needs dedicated educational actions to support proper nutritional habits. Additionally, older age, living in a rural environment, being underweight and overweight/obese, and having a low physical activity level may be indicated as factors predisposing one to food preferences potentially promoting unhealthy dietary habits.