In Pinus pinea, cone to pine nut yield (total pine nut weight expressed as percentage of cone weight), an important crop trait, is decreasing worldwide. This phenomenon is of great concern, since the nuts of this species are highly demanded. Cone weight, seed and pine nut morphometry, and pine nut yield were monitored in a non-native area in Chile for 10 years. For this purpose, 560 cones, and the seeds and pine nuts contained in them, were counted, measured and weighed in a multi-environment study involving seven plantations. Seed and pine nut damage was evaluated. Two contrasting categories of cone weight (heavy/light) were defined. Cone to pine nut yield (PY) and other traits were calculated and compared between categories using a mixed linear model. Regression trees were used to explain PY variability. Cone weight was higher than in the species’ native range (474 g vs 300 g on average). Pine nut number per cone and PY were significantly higher in the heavy cone category than in the light cone category (125 vs 89 units, and 4.05 vs 3.62%, respectively), The percentage of damaged seeds was lower in heavy than in light cones (9.0% vs 15.9%). Thus, PY depended on seed and pine nut morphometry as well as on seed health. Management practices, such as fertilization and irrigation, could be used to boost production of heavy cones and consequently increase PY.