Anthocyanins are colorful plant pigments with antioxidant properties, and a diet rich in these ‎flavonoids bears health benefits. Therefore, a strong anthocyanin accumulation in edible plant ‎parts is of significant interest, and in Malus domestica, the domesticated apple, certain red-fleshed ‎apple varieties exhibit this trait. Enhanced anthocyanin accumulation in the flesh of apple fruits is ‎attributed to the hyperactivation of the MYB transcription factor MdMYB10, which act as a key ‎regulators of anthocyanin biosynthesis by inducing the expression of multiple biosynthetic genes. ‎While several studies have explored the underlying genetic mutations and resulting transcriptome ‎changes, there is a lack of research on proteome alterations that cause the red-fleshed apple ‎phenotype. To address this gap, a mass spectrometry-based proteomics approach was employed. ‎Comparative proteomics identified differentially abundant proteins in young and mature fruits of the ‎red-fleshed ‘Bay13645’ variety compared to the white-fleshed ‘Royal Gala’. Whereas several MYB ‎transcription factors were enriched during early fruit development, they were no longer among the ‎hyper-abundant proteins in ripe fruits of the red-fleshed genotype. In contrast, anthocyanin ‎biosynthetic enzymes were enriched more strongly in ripe fruits of the red-fleshed cultivar, ‎indicating developmental stage-specific differences in the control of the pigmentation process. The ‎proteomic approach also identified novel regulatory factors and enzymes that may contribute to the ‎red-fleshed apple phenotype, including a BAHD acyltransferase, Mal d proteins, and transcription ‎factors of diverse families, and their potential relevance for the exhibition of this trait is discussed.‎