Fruit quality traits are directly linked to consumer acceptability, and thus key targets for banana breeding programs. We explored the genetic control of three major organoleptic and ripening-related traits, namely pulp acidity (pH), firmness (PF) and dry matter content (DMC), over a 7-day ripening period and three production cycles in a banana segregating population genotyped by sequencing. Significant broad-sense heritabilities were estimated with 0.77, 0.46 and 0.81 values for pH, PF and DMC, respectively. QTL detection was first performed on the whole dataset to analyze their dynamics. In a second approach, per-cycle data were considered to evaluate the stability across production cycles. Finally, a meta-analysis was performed. Various QTLs were detected, as well as many QTL colocalizations, while 12 of these QTLs were more prominent as they were detected in several approaches and/or explained over 15.0% of the phenotypic variation. Candidate genes were proposed for 10 of these QTLs. The QTL with the largest contribution to pulp acidity (R2 = 19.3–50.6%) was located on LG1_7 on the genetic map of Pisang Madu, i.e. a parent that is closely related to Cavendish, the world's most cultivated dessert banana cultivar group. This QTL is located on a chromosome derived from a reciprocal translocation that does not recombine in Pisang Madu, which is a favorable context for molecular marker monitoring. These first results will provide a relevant basis for marker-assisted selection in banana improvement programs.