Background: The COVID-19 pandemic has impacted children’s lifestyles, including dietary behaviors. Of particular concern among these behaviors is the heightened prevalence of ultra-processed food (UPF) consumption, which has been linked to the development of obesity and related non-communicable diseases. The present study examines the changes in (1) UPF and (2) vegetable and/or fruit consumption among school-aged children in Greece and Sweden before and during the COVID-19 pandemic. Methods: The analyzed dataset consisted of main meal pictures (breakfast, lunch, and dinner) captured by 226 Greek students (94 before the pandemic and 132 during the pandemic) and 421 Swedish students (293 before and 128 during the pandemic), aged 9–18, who voluntarily reported their meals using a mobile application. The meal pictures were collected over four-month periods over two consecutive years; namely, between the 20th of August and the 20th of December in 2019 (before the COVID-19 outbreak) and the same period in 2020 (during the COVID-19 outbreak). The collected pictures were annotated manually by a trained nutritionist. A chi-square test was performed to evaluate the differences in proportions before versus during the pandemic. Results: In total, 10,770 pictures were collected, including 6474 pictures from before the pandemic and 4296 pictures collected during the pandemic. Out of those, 86 pictures were excluded due to poor image quality, and 10,684 pictures were included in the final analyses (4267 pictures from Greece and 6417 pictures from Sweden). The proportion of UPF significantly decreased during vs. before the pandemic in both populations (50% vs. 46%,p= 0.010 in Greece, and 71% vs. 66%,p< 0.001 in Sweden), while the proportion of vegetables and/or fruits significantly increased in both cases (28% vs. 35%,p< 0.001 in Greece, and 38% vs. 42%,p= 0.019 in Sweden). There was a proportional increase in meal pictures containing UPF among boys in both countries. In Greece, both genders showed an increase in vegetables and/or fruits, whereas, in Sweden, the increase in fruit and/or vegetable consumption was solely observed among boys. Conclusions: The proportion of UPF in the Greek and Swedish students’ main meals decreased during the COVID-19 pandemic vs. before the pandemic, while the proportion of main meals with vegetables and/or fruits increased.