Heterocyclic amines (HAs) are formed as Maillard reaction products in the crust of meat products during heating processes. Two typical pizza toppings—salami and cooked ham—were analyzed for the presence of HAs after baking frozen pizzas at top and bottom temperatures of 250 and 230 °C, respectively. After baking pizza slices for 12 min, MeIQx (2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline; 0.2 ng/g), 4,8-DiMeIQx (2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline; 0.5 ng/g), PhIP (2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine; 0.2 ng/g), norharman (4.5 ng/g), and harman (2.5 ng/g) were found in the ham toppings, whereas only the comutagenic norharman (107.4 ng/g) and harman (11.4 ng/g) were found in the salami toppings. The content of MeIQx and 4,8-DiMeIQx in ham increased from 0.3 to 1.8 ng/g and 0.8 to 1.6 ng/g, respectively, when the recommended baking time was increased from 15 min (manufacturer's specification) to 18 min at 230 °C. MeIQx was formed in salami when the heating time was extended to 18 min. Moreover, higher concentrations of PhIP in salami or ham slices were found when baking temperatures were 250 °C rather than 230 °C (baking time of 12 min). However, sensory tests showed that panelists preferred longer-baked pizzas due to an increased crispiness. Thus, results show that a substantial formation of HAs may occur in pizza toppings such as ham and salami, with ham being particularly susceptible when compared to salami. Formation of HAs increases with increasing baking time and temperature. The occurrence of the cupping of ham or salami slices during baking may also increase the formation of HAs.