To investigate the main motives driving dietary intake changes potentially introduced by preventive measures to address the pandemic, an online survey, using a 36-item Food Choice Questionnaire applied for the period before (the year 2019) and during (2020–2021) the pandemic, was distributed between July and October 2021 among adult residents from Belgium. A total of 427 eligible respondents, the majority Dutch-speaking, were included for analyses. The importance of nine motives for food choices, including health, mood, convenience, sensory appeal, natural content, price, weight control, familiarity and ethical concerns, was assessed by scoring from 1 to 5, and comparing mean scores from the during period with the before period. Sensory appeal was the most important food choice motive before (mean score of 4.02 ± 0.51) and during (3.98 ± 0.48) the pandemic. Convenience and health also ranked among the main motives, with health observed to become more important during the pandemic (3.69 ± 0.60 during vs. 3.64 ± 0.59 before). Additionally, mean scores of mood (3.41 ± 0.71 vs. 3.32 ± 0.58), natural content (3.35 ± 0.84 vs. 3.26 ± 0.85) and weight control (3.33 ± 0.79 vs. 3.25 ± 0.76) were significantly higher during as compared to before. The extent of change in the level of importance for natural content was smaller with increasing age, and for health larger for urban areas, but for other motives there were no significant differences across population subgroups. Changes in the level of importance were observed in both directions, while a moderate share of respondents declared no change, suggesting some persistence of food choice motives. Further activities within public health monitoring should be considered to fully understand the COVID-19 implications on food choice motives together with people’s food behaviors and consumption.