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Rapid softening is one of the main problems of soursop (Annona muricata L.) fruits. The physicochemical parameters and gene expression response of cell-wall-related genes in soursop fruits were evaluated. The temperature of 15 ± 2 °C delayed the physicochemical composition of soursop fruits by three days and significant down- regulated the expression of cell-wall related genes. Pectin methylesterase (PME1), pectate lyase (PL22), polygalacturonase (PG), Endoglucanase (EG), and expansins (EXP13 and EXP7) genes showed a down-regulation of their expression during ripening at 28 ± 2 °C and 15 ± 2 °C. The bioinformatic analysis demonstrated two conserved domains associated with degradation of cell wall. Higher gene level of the EXP7 gene was detected on Day 6 of storage at 28 ± 2 °C, showing a 3.5-fold increase in the gene expression compared to Day 0. Furthermore, PME1, PL22, PG, EG, and EXP13 expression was down-regulated by the temperature of 15 ± 2 °C (p < 0.05). Gene expression was highly correlated in the fruits stored at 28 ± 2 °C. On the other hand, a high correlation between the EXP7, PME1, and PL22 genes was recorded on the fruits stored at 15 ± 2 °C. The multivariate analysis demonstrated that acidity is an important variable during ripening and the two EXP genes, and EG are highly correlated with acidity and negatively correlated with firmness. In conclusion, the findings of this research suggest that these genes are down-regulated by the combination of days of storage and temperature. [ABSTRACT FROM AUTHOR]