Core Ideas A gene bank of heritage apple cultivars with historical data proves suitable for GWAS. GWAS showed associations between acetate esters and AAT1 and nearby paralogues. Sugar content and sugar composition associates with a vacuolar invertase gene. Harvest date correlates with a certain haplotype of the NAC18.1 transcription factor. Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple (Malus domestica L.) cultivars. We linked genotype and phenotype information by combining genotyping‐by‐sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography–mass spectrometry (GC‐MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl‐transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker‐assisted selection (MAS).