Pediatric food allergies (FAs) are health conditions that adversely impact the quality of life of children and their caregivers. Aim: The primary objective of the present study was to assess the quality of the diets administered to allergic children based on the Healthy Diet Index (HID-10), to determine the influence of parental knowledge about FAs and the elimination diet, and to identify the factors that contribute to healthy food choices. Material and Methods: This study was conducted as part of the “Living with an Allergy” research and educational program for preschool children, which was implemented between June 2021 and June 2023 in the city of Lublin. Results: Food allergies were diagnosed and confirmed in 241 children, including 106 boys (44%). A higher number of unhealthy dietary factors (DQI-1) was significantly associated with gender, and lower DQI values were more often noted in boys (p < 0.05). In turn, a higher number of health-promoting dietary factors (DQI-3) was significantly associated with a younger age in children (OR 1.54; 95%CI 1.17–1.74, p < 0.01) and with an older age in parents (OR 1.43; 95%CI 1.2–1.67, p < 0.05). Conclusions: Children whose diets, including the necessary modifications, were recommended by a physician or a dietitian were characterized by significantly higher DQI values and a higher number of health-promoting dietary factors. The diets of children with FAs should consist mainly of unprocessed foods to control the intake of unhealthy products that suppress immunity.