The development of new varieties combining complementary molecular mechanisms is hypothesized to enhance the durability of genetic resistance to apple scab. However, both the underlying mechanisms and the efficiency of their pyramiding are still unknown. To further understand the molecular mechanisms of resistance to the fungus Venturia inaequalis (responsible of apple scab), we explored apple specialized metabolism through an untargeted metabolomic approach of a pseudo-F1 progeny, known as the ‘TxF progeny’. This progeny was previously widely investigated for its favourable resistance alleles and four segregating quantitative trait loci (QTL) were described. To identify metabolites associated with resistance conferred by each QTL, a total of three experiments have been conducted in a greenhouse environment on this progeny. The datasets include raw metabolomic profile descriptions of three experiments with or without experimental inoculation of Venturia inaequalis.