Mapping studies using populations with introgressed marker-defined genomic regions are continuously increasing knowledge about quantitative trait loci (QTL) that correlate with variation in important crop traits. This knowledge is useful for plant breeding, although combining desired traits in one genotype might be complicated by the mode of inheritance and co-localization of QTL with antagonistic effects, and by physiological trade-offs, and feed-back or feed-forward mechanisms. Therefore, integrating advances at the genetic level with insight into influences of environment and crop management on crop performance remains difficult. Whereas mapping studies can pinpoint correlations between QTL and phenotypic traits for specific conditions, ignoring or overlooking the importance of environment or crop management can jeopardize the relevance of such assessments. Here, we focus on fruit load (a measure determining competition among fruits on one plant) and its strong modulation of QTL effects on fruit size and composition. Following an integral approach, we show which fruit traits are affected by fruit load, to which underlying processes these traits can be linked, and which processes at lower and higher integration levels are affected by fruit load (and subsequently influence fruit traits). This opinion paper (i) argues that a mechanistic framework to interpret interactions between fruit load and QTL effects is needed, (ii) pleads for consideration of the context of agronomic management when detecting QTL, (iii) makes a case for incorporating interacting factors in the experimental set-up of QTL mapping studies, and (iv) provides recommendations to improve efficiency in QTL detection and use, with particular focus on model-based marker-assisted breeding.