Allergen sensitization profiles are increasingly affected by environmental and climate changes. This study exemplifies fundamental differences in molecular IgE sensitization profiles in two nearby regions in Argentina with different climatic conditions (La Plata and Bahía Blanca). A cross-sectional study was conducted involving 155 patients with allergic symptoms from La Plata and Bahía Blanca (34.0 ± 11.2 years, female/male: 83/72). Serum samples were analyzed for IgE reactivity using a chip containing 101 micro-arrayed allergen molecules. Statistical analyses were performed to compare allergen-specific IgE levels, sensitization prevalences and reported symptoms. Patients from La Plata—with subtropical weather—showed a higher prevalence of IgE reactivity to house dust mite (HDM) allergens (Der p 23: 74%; Der p 1: 53% and Der p 2: 56%) and more frequently reported asthma (AS) symptoms (40% vs. 24%) than patients from Bahía Blanca. In contrast, patients from Bahía Blanca, with dry and windy weather, exhibited higher sensitization rates to pollen allergens, particularly Phl p 1 (49%) and Ole e 1 (22%) as well as to Alternaria alternata (Alt a 1, 35%) and reported a significantly higher prevalence of skin manifestations (54% vs. 31%) than those from La Plata. Cat allergen Fel d 1 was an equally important sensitizer in both regions (La Plata 30% and Bahía Blanca 37%). Sensitization to class 1 food allergens was rare in both groups (1–8%), including non-specific lipid transfer proteins (peanut Ara h 9 and peach Pru p 3) but IgE sensitizations to genuine peanut allergens were almost absent. Important regional differences in allergen sensitization profiles were observed between two geographically close regions with different climatic conditions. Our findings underscore the relevance of region-specific allergen profiling and highlight the clinical utility of molecular allergy diagnosis for a more precise allergen identification and improved management of allergic diseases.