Ultra-processed foods’ (UPFs’) consumption has been positively linked to the presence of allergic symptoms, but it is yet unknown whether this is linked to their nutritional composition or allergen load. This study used the ingredient lists available in the Greek Branded Food Composition Database, HelTH, to classify foods (n =4587) into four grades of food processing (NOVA1–4) according to the NOVA System. Associations between NOVA grades and the presence of allergens (as an ingredient or trace) were studied. Overall, UPFs (NOVA4) were more likely to contain allergens than unprocessed foods, NOVA1 (76.1% vs. 58.0%). However, nested analyses among similar foods showed that in >90% of cases, processing degree was not linked to allergens’ presence. Recipe/matrix complexity was more strongly linked to allergens’ presence with NOVA4 foods declaring 1.3 allergenic ingredients vs. 0.4 allergenic ingredients in NOVA1 foods (p< 0.01). Exposure to trace allergens was more common for NOVA4 than NOVA1 foods (45.4% vs. 28.7%), but the extent of contamination was similar (2.3 vs. 2.8 trace allergens). Overall, UPFs are more complex mixtures with higher numbers of allergens per food and are more prone to cross-contamination. However, indicating a food’s degree of processing is not sufficient to help identify allergen-free choices within the same subcategory.