Site-quality is a major determinant of fitness but its effect can be confounded by individual quality, a relationship that has been little studied in large, long-lived vertebrates. The fitness effects of quality estimates depend on the assumption of co-variation between individual and territory quality and can be framed as five working hypotheses: no effect on fitness, exclusive effect of individual quality, exclusive effect of site quality, and independent or interactive effects of the two. We explored such a framework using a medium-sized raptor, the black kite Milvus migrans, as a model species. Individual and territory quality co-varied, but the strength of the relationship varied across different estimates of individual quality (age, body size, or mass residuals). Short-term production of fledglings was related to the independent effects of both individual and territory quality. However, longer-term production of recruits was related solely to territory quality. The disappearance of individual quality effects over the long-term may be caused by antagonistic selective pressures acting during different stages of the life cycle. Our results contribute to a growing appreciation of the long-term fitness-benefits of advantages experienced in early life and highlight the importance of a long-term perspective in studies assessing the effects of individual and territory quality. In our case study, prioritizing sites for conservation on the basis of territory quality may be a feasible pathway to maintain the viability of the population. However, scenarios where such a method could be inefficient have been previously reported, suggesting caution in its application. More studies are needed to understand the generality of the efficiency of priority-setting approaches based on site quality.