Hass avocado postharvest ripening heterogeneity creates several logistics problems at destination markets. Although several approaches mainly based on targeted analysis have been undertaken to broaden our understanding of the potential causes of this postharvest ripening heterogeneity, still the secret is not yet unveiled. In this study biopsies from individual fruit displaying contrasting ripening behavior (slow vs fast) and subjected to different storage conditions (immediately after harvest, 30 d regular air at 5 °C and 30 d at 5 °C and 4 kPa O2 and 6 kPa CO2) were analyzed for targeted fatty acid analysis and cell wall enzyme activity combined with a more integrative approach based on gel free proteomics LC–MS/MS. The high throughput proteomics was capable of discriminating between slow and fast ripening avocado fruit. Proteins that were mainly less abundant in the slow ripening phenotype were annotated to correct protein folding, translation and de novo synthesis and higher abundant proteins were annotated to amino sugar and nucleotide metabolism, detoxification and stress response and proteolysis. Our study opens new insights into the causes of heterogeneous ripening and may provide new markers for avocado ripening at harvest and after prolonged storage.