Sweetness is one of the most important fruit quality traits in breeding programs, determining the overall quality and flavor perception of apples. Selecting for this trait using conventional breeding methods is challenging due to the complexity of its genetic control. In order to improve the efficiency of trait selection via DNA-based markers, extensive studies focused on the detection of quantitative trait loci (QTL) and the development of DNA-based markers associated with QTL regions for traits of interest. Newly discovered QTLs detected in multiple apple breeding populations are presented here for individual sugars (fructose, glucose, sucrose, and sorbitol) and soluble solids content (SSC) at harvest, after 10, and 20 weeks of refrigerated storage followed by 1 week at room temperature in two successive years. A total of 1416 polymorphic SNPs were filtered from the RosBreed Apple SNP Infinium® array for QTL analysis using FlexQTL™ software. QTLs for individual sugars were identified on linkage groups (LG) 1, 2, 3, 4, 5, 9, 11, 12, 13, 15, and 16, and QTLs for SSC were found on LGs 2, 3, 12, 13, and 15. One QTL region on LG 1 was consistently identified for both fructose and sucrose from harvest through storage in both years, which accounted for 34–67 and 13–41 % of total phenotypic variation, respectively. These stable QTLs with high explained phenotypic variation on LG 1 for fructose content indicate a promising genomic region for DNA-based marker development to enable marker-assisted breeding for sweetness selection in apple breeding programs.