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Red-flesh color development in apple fruit is known to depend upon a particular allele of the MdMYB10 gene. While the anthocyanin metabolic pathway is well characterized, current genetic models do not explain the observed variations in red-flesh pigmentation intensity. Previous studies focused on total anthocyanin content as a phenotypic trait to characterize overall flesh color. While this approach led to a global understanding of the genetic mechanisms involved in color expression, it is essential to adopt a more quantitative approach, by analyzing the variations of other phenolic compound classes, in order to better understand the molecular mechanisms involved in the subtle flesh color variation and distribution. In this study, we performed pedigree-based quantitative trait loci (QTL) mapping, using the FlexQTL™ software, to decipher the genetic determinism of red-flesh color in five F1 inter-connected families segregating for the red-flesh trait. A total of 452 genotypes were evaluated for flesh color and phenolic profiles during 3 years (2021–2023). We identified a total of 24 QTLs for flesh color intensity and phenolic compound profiles. Six QTLs were detected for red-flesh color on LG1, LG2, LG8, LG9, LG11, and LG16. Several genes identified in QTL confidence intervals were related to anthocyanin metabolism. Further analyses allowed us to propose a model in which the competition between anthocyanins and flavan-3-ols (monomer and oligomer) end-products is decisive for red-flesh color development. In this model, alleles favorable to high red-flesh color intensity can be inherited from both white-flesh and red-flesh parents.