The aim of the study was to optimize the conditions [inoculum size (4, 6, and 8%), fermentation temperature (31, 34, and 37 °C), and apple: tomato ratio (2:1, 1:1, and 1:2)] on the viable cell count and sensory evaluation in apple–tomato pulp by response surface methodology (RSM), and determine the physicochemical properties, antioxidant activity, and sensory properties during fermentation. The optimal treatment parameters obtained were an inoculum size of 6.5%, a temperature of 34.5 °C, and an apple: tomato ratio of 1:1. After fermentation, the viable cell count reached 9.02 lg(CFU/mL), and the sensory evaluation score was 32.50. During the fermentation period, the pH value, total sugar, and reducing sugar decreased by 16.67%, 17.15%, and 36.05%, respectively. However, the total titratable acid (TTA), viable cell count, total phenol content (TPC), and total flavone content (TFC) increased significantly by 13.64%, 9.04%, 21.28%, and 22.22%, respectively. The antioxidant activity [2,2-diphenyl-1-picrylhydrazyl (DPPH) free-radical scavenging ability, 2,2′-azino-di(2-ethyl-benzthiazoline-sulfonic acid-6) ammonium salt (ABTS) free-radical scavenging ability, and ferric-reducing antioxidant capacity power (FRAP)] also increased by 40.91%, 22.60%, and 3.65%, respectively, during fermentation. A total of 55 volatile flavour compounds were detected using HS-SPME-GC–MS among the uninoculated samples and fermented samples before and after fermentation. The results showed that fermentation increased the types and total amount of volatile components in apple–tomato pulp, and eight new alcohols and seven new esters were formed. Alcohols, esters, and acids were the main volatile components in apple–tomato pulp, accounting for 57.39%, 10.27%, and 7.40% of the total volatile substances, respectively.