Avocado (Persea americana) production is nowadays questioned due to its environmental impact, especially water footprint. Avocado rootstocks have been developed to enhance the resistance to environmental conditions but not for resource efficiency. In this study, physiological parameters of 18 months old vegetatively(clonally-) propagated (Dusa®) and seed-propagated (Mexicola) rootstocks grafted with 'Hass' avocado in a controlled environment (substrate and greenhouse) were investigated over 90 weeks in central Chile. Differences in aerial and root growth and root type (rhizotrons) parameters, water and nutrient (nitrate and phosphate) use efficiency and main non-structural carbohydrates (glucose, fructose, sucrose, mannoheptulose, perseitol and starch) were measured for both evaluated rootstocks in the vegetative and flowering periods. Principal component analysis (PCA) revealed differences between rootstocks and phenological periods. Clonally-propagated rootstocks were characterized by higher root growth while seed-propagated rootstocks were characterized by aerial growth and high carbohydrate contents in the roots. Meanwhile water and nutrient use efficiency was only associated with the phenology but not to rootstock type. With the same water and nutrient consumption, Mexicola rootstocks achieved higher biomass production and carbohydrate accumulation in the roots which could be beneficial for successful flowering and fruit bearing. These results provide evidence of the importance of considering the resource and environmental efficiency to inform the selection process of modern rootstocks; decision-making that currently ignores such important pieces of information.