A fruit tree breeding program requires heritable variation at both, the rootstock and the scion level, upon which selection can act. Avocado trees (Persea americana) originated in the neotropics and do not exhibit the characteristic genetic bottleneck of many other crops. The incipiency in this domestication has prevented the selection of desirable traits, particularly at the rootstock level. Therefore, our goal was to quantify the inheritance of rootstock effects in scion traits in avocado cv. Hass. We characterized 349 rootstocks from 8 avocado cv. Hass plantations in three regions in the province of Antioquia, in the northwest Andes of Colombia, using 13 microsatellite markers (SSRs). Parallel to this, 21 phenotypic traits (including yield, fruit quality, and morphological and eco-physiological traits) were recorded in the scions during 3 years (2015-2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in an animal-model in order to calculate narrow-sense heritabilities (h2) on scion traits. Heritability estimates were significant for 5 of the measured traits and ranged from 0.58 to 0.74 with model fits (R2) ranging from 0.52 to 0.85 across plantations. The results showed significance in the rootstock effects for various quality and ripening traits (i.e. total number of fruits, number of fruits with low weight, number of fruits damaged by trips, and number of fruits with exportation quality), while for morphological traits the only one we found having a significant heritability value was trunk height. These findings suggest the inheritance of rootstock effects on a surprisingly wide spectrum of scion traits in avocado. Furthermore, this research is, up to date, the most cohesive evidence of inheritance of rootstock effects in any fruit tree. Ultimately, this work reinforces the importance of considering the rootstock-scion interaction to enhance our understanding of the consequences of grafting and speed up fruit tree breeding programs.