The contamination and spoilage of heat-treated fruit juices by heat-resistant mold ascospores present significant challenges to the food industry. Understanding effective strategies to mitigate this contamination is vital for ensuring the shelf-life and microbial safety of heat-treated fruit juices. This study investigated the thermal resistance of ascospores from different heat-resistant mold species, including Aspergillus laciniosus, A. chevalieri, A. denticulatus, A. siamensis, Hamigera pallida, and Talaromyces macrosporus, isolated from pineapple and sugarcane field soils. Ascospores inactivation kinetics in pineapple juice under heat treatment (75–97 °C) were analyzed using log-linear and Weibull models. Among these species, A. laciniosus displayed the highest heat resistance (δ-value: 104.59 min at 85 °C), while A. siamensis exhibited the lowest (δ-value: 3.39 min at 80 °C). Furthermore, A. laciniosus, the most heat-resistant species, showed notable tolerance to sanitizers. The most effective inactivation was achieved using 1.0% (w/v) sodium hypochlorite for 15 min. Chlorine dioxide, however, was generally ineffective and even activated dormant ascospores in some cases. The combination of hot water (65 °C for 5 min) with sanitizer increased ascospore reduction in most species but did not achieve the 3-log reduction required by the European Standard N13697. This study revealed a correlation between ascospore resistance to heat and chlorine dioxide, offering significant findings for practical inactivation strategies.