Two autotetraploid (4×) trifoliate orange (Poncirus trifoliata (L.) Raf.) rootstocks and the corresponding diploid (2×) rootstocks were compared for their impact on clementine "Commune" (Citrus clementina Hort. ex Tan) production and on rootstock/scion physiology. Cumulative fruit yield, fruit quality (sugars, organic acids, carotenoids, hesperidin) and scion physiology (stem growth, leaf starch, sugars, chlorophyll content, phenolic content and gas exchange parameters) were investigated. The cumulative fruit yield over 11 years was lower in 4× rootstock/clementine associations and correlated with reduced vigor of the clementine scion. Fruit quality criteria were not affected by the ploidy level of the rootstocks, with the exception of hesperidin content, which was higher with 4× than 2× rootstock/clementine associations. Leaf chlorophyll and phenolic contents were higher with 4× than 2× rootstock/clementine associations. In leaves, the rate of photosynthesis and stomatal conductance was much higher with 2× rootstocks; however, the maximum electron transport rate was lower when compared to the 4× rootstocks. Similarly, leaf starch and sugar contents were much higher with 4× than 2×. Taken together, these results demonstrate that the use of 4× rootstocks dramatically changes both tree physiology and fruit yield, without promoting large changes in fruit quality criteria.