Despite growing demand for more healthful frozen pizza, current technologies for increasing potential healthfulness such as reformulation or enrichment of raw ingredients may lead to undesirable changes in the final product. This study evaluated alternative heat treatments of selected frozen pizza ingredients as methods for increasing the healthfulness of frozen pizza. Four common vegetable toppings (i.e., onion, corn, Japanese green pepper, and red pepper) were heated on a 250°C hot plate, and commercially available par‐baked pizza base was reheated at 500°C for 50 s to induce browning. These alternatively heat‐treated (AHT) ingredients were compared to their conventional counterparts (e.g., steam‐blanched vegetable toppings and commercially available par‐baked pizza base, respectively) in terms of total polyphenol content (TPC) and 2,2‐diphenyl‐1‐picrylhydrazyl radical scavenging activity (DPPH RSA). TPC increased and was correlated with internal temperature for onion and peppers during alternative heat treatment, while increases in DPPH RSA of AHT onion and pizza base may be due to the formation of Maillard reaction products. Replacing conventional samples with AHT counterparts increased TPC and DPPH RSA by 1.2‐fold to 1.6‐fold and 1.3‐fold to 2.1‐fold, respectively, for vegetable toppings after reheating at 230°C for 12 min. Significant differences in acceptability of sensory attributes (i.e., appearance, taste, aroma, texture, and overall preference) were not observed between AHT and conventional vegetable topping when incorporated into pizza. These results suggest that alternative heat treatment of raw ingredients, particularly vegetable toppings, for the purpose of increasing TPC and DPPH RSA may be a viable method for increasing the potential healthfulness of frozen pizza.