The choice of rootstock has a significant impact, not only on fruit growth and development, but also on avocado fruit quality and postharvest performance. The objective of this study was to evaluate and compare attributes related to the postharvest quality of Hass avocados from “Mexicola” and “Duke 7” rootstocks grown under similar conditions. This study included two harvests: early (23–26% dry matter) and middle (>26–30% dry matter) per season for the 2016/2017 and 2017/2018 seasons and two storage conditions (regular air (RA) at 5 °C and controlled atmosphere (CA) at 4 kPa O2 and 6 kPa CO2 at 5 °C) for 55 days. The results showed significant differences in firmness, color and vascular and flesh browning between storage conditions; in addition to these last three attributes, the rootstock played an important role. The fatty acid profile did not reveal significant differences between fruit from both rootstocks. Finally, the polar metabolite profiles revealed differences only for the storage condition, not associated to the rootstock, which could affect the postharvest performance of Hass avocado fruit. This study is one of the few available showing the interaction of rootstock/Hass cultivar on fruit quality and postharvest performance.