Stone pine (Pinus pinea) grows in natural stands within the Mediterranean basin and its nut is highly appreciated for its nutritional profile. Nevertheless, a decline in this species due to biotic and abiotic damages is currently being clearly observed. This situation has led to its development as a nut crop, to try to save its production and obtain regular harvests over the years. Under this agronomic scenario, the aim of this work was to compare the behavior of the stone pine grafted onto two rootstocks, P. pinea (PP) and P. halepensis (PH), by evaluating cone productivity, tree growth response, mast seeding patterns and pine nut composition. The field test was composed of 14 PH and 14 PP, randomly distributed into groups of 4–5 trees/rootstock. Data were from seven productive growing seasons. The results show higher growth and ripe cone production on PP rather than PH, although the productivity (cones/m2 canopy) was similar. Any effect of rootstock was observed on the mast seeding pattern and weight of cones, while the pine nut composition showed differences in the fatty acids content. The global quality of production was similar in PH and PP.