Main determinants of ‘Hass’ avocado quality and consumer acceptance are mesocarp firmness and skin color. Relevant producing and exporting countries have evidenced during the last seasons color desynchronization with softening at edible ripeness. The mechanisms driving this desynchronization are still unknown. Thus, this study aimed to provide a first deep insight into this problem by combining targeted pigment, hormone and gene expression analysis in avocado exocarp samples from different harvests and storage conditions. Results showed that color desynchronization was more pronounced in regular air (RA) condition and early harvest for all orchards. Prolonged controlled atmosphere (CA) storage synchronized color development in all orchards analyzed. Chlorophylls and carotenoids did not decrease in content as the fruit reached the ready to eat stage but remained stable while total anthocyanins increased in all evaluated orchards. Total anthocyanins and abscisic acid were strongly and positively correlated with the “black color” phenotype. The other evaluated hormones (JA, IAA, SA, tZ, DHZ, iP) revealed negative correlations with the “black color” phenotype. Gene expression related to the ethylene biosynthesis pathway (PamACS, PamETR avocado gene orthologues) showed an up-regulation in fruit phenotyped as ready to eat (RTE) Green. In addition, the expression of the genes orthologues PamPAL, PamF3H and PamCHS was also positively correlated with anthocyanin content in the skin. Our results revealed that color desynchronization with softening of ‘Hass’ avocado is quite complex in terms of hormonal interplay and the role of storage conditions (RA vs CA). Thus, further studies need broader approaches such as the incorporation of omics studies to elucidate the physiological and molecular mechanisms driving color desynchronization.