The objective of this study was to identify transcripts or hormone-based biomarkers to define the physiological age of ′Hass′ avocado fruit and to elucidate the changes at the level of metabolic pathways and their regulation. ′Hass′ avocado fruit from orchards in different agroclimatic zones were collected during two harvest periods. Fruit were stored for 30 d under controlled atmosphere and regular air conditions and then transferred to shelf-life conditions at 20 °C. The physiological age as represented by the initial state of a hypothetical enzyme system (E0) of each fruit was obtained through a mechanistic softening model for Chilean ′Hass′ avocado previously developed. Fruit from three different E0 ranges (low, intermediate and high) were selected for transcriptome and hormone analyses. Sequencing data were processed by partial least squares regression analysis, which revealed 46 genes correlated to E0. Different metabolic pathways were over expressed between low and high E0 fruit. Low E0 fruit showed overexpression of genes related to DNA replication, auxin transport, cell wall remodeling, gibberellin synthesis, brassinosteroids and flavonols. On the other hand, fruit with high E0 revealed genes related to ethylene and abscisic acid biosynthesis and related responses and phenylpropanoid biosynthesis. Likewise, targeted hormone analysis revealed higher concentrations of active gibberellins (GA1 and GA4) and jasmonic acid for low E0 fruit and for high E0 fruit higher concentrations of abscisic acid, salicylic acid, dihydrozeatin, indole acetic acid and trans-zeatin, only the latter two being significant for this phenotype. This study reveals the relationship between transcripts and hormones during fruit maturation that is key to evaluate the physiological age of ′Hass′ avocado fruit.