Background Diagnosis of food allergies is challenging, as combining information from specific IgE (sIgE)‐sensitization pattern and skin prick tests (SPTs) with clinical history is necessary for a personalized management of allergic patients. The aim of this study was to compare two molecular tests, the ImmunoCAP ISAC (ISAC) and the Allergy Explorer, version 2 (ALEX2) in the context of pollen food syndrome (PFS) diagnosis in a real‐life scenario, to assess the benefit of multiplex testing in PFS patients. Methods Diagnosis of food allergy was performed in 53 patients. Allergen‐sIgE concentrations were measured with ISAC and ALEX2. Results for sIgE were statistically compared with each other, with SPT results and with clinical presentation of the patients. Results Using ISAC as reference test for sIgE measurements, the average sensitivity of ALEX2 for PR‐10 allergens was 83.2% and the average specificity 88.0%. If only low sIgE concentrations were included, the sensitivity was 60.8% and the specificity 91.1%. Apple and hazelnut sensitizations were confirmed in most patients by concordance of sIgE and SPT results. Significant correlations were shown between clinical symptoms and Mal d 1‐ and Gly m 4‐sIgE levels measured by both tests and for Cor a 1‐sIgE levels measured by ALEX2. In eight patients, profilin related symptoms were supported by Hev b 8‐sensitization. Conclusion Multiplex testing is beneficial to understand patient‐specific individual sensitization profiles and to providing personalized management recommendations. In the future, custom‐designed test kits might enable reducing costs of multiplex testing for specific patient groups without compromising the diagnostic value.