The objective of this study was to investigate the effect of thermal processing on the chemical quality and sensory characteristics of Annona squamosa L. and Annona muricata L. fruit pulps and nectar. The fruit pulps were pasteurized at 85 °C for 20 min and nectar prepared as per Food Safety and Standards Authority of India (FSSAI) specifications. The chemical composition of fresh and heated pulps of A. squamosa and A. muricata showed that compared to fresh, the chemical profile and sensory profile changed in heated samples and nectar. The free and bound phenolics of A. squamosa increased in heated pulp (127.61 to 217.22 mg/100 g and 150.34 to 239.74 mg/100 g, respectively), while in A. muricata, free phenolics increased very marginally from 31.73 to 33.74 mg/100 g and bound phenolics decreased from 111.11 to 86.91 mg/100 g. This increase in phenolic content may be attributed to the perception of bitterness and astringency in A. squamosa pulp on heating. In electronic tongue studies, principal component analysis (PCA) confirmed that the fresh and heated pulps had different scores, as indicated by sensory analysis using qualitative descriptive analysis (QDA). E-tongue analysis of samples discriminated the volatile compounds released from the heated A. squamosa and A. muricata fruit pulps and nectar in their respective PCA plots by forming different clusters.