Sorghum is an important and versatile food crop in the Sudan savannah environments of West Africa. Sorghum production doubled in the last 20 years and its yield remained stable and low in Mali. Molecular markers were used to dissect quantitative variation to increase efficiency of breeding programs. From 2009–2014, marker-assisted recurrent selection (MARS), an integrated process to identify favorable alleles and to monitor their pyramiding throughout the breeding course, was implemented. Two large bi-parental populations derived from complementary recent elite inbreds, Tiandougou, Keninkeni, and Lata-3, were developed to improve grain yield productivity and stability while maintaining traditional food processing quality. Populations were phenotyped multi-locally. Quantitative Trait Loci (QTL) analyses identified, in each genomic region, the most favorable morphologic, yield components, grain quality, and flowering time parental alleles. Marker-assisted recurrent selection approach is detailed for one of the populations. Several genotypic ideotypes corresponding to ideal recombination patterns between the parents were defined. Molecular marker-guided recurrent crossing allowed favorable QTL accumulation for a large range of traits. Three marker-assisted recurrent selection cycles were accomplished. Four stable and superior elite lines were identified, leading to their registration in 2018 in national and ECOWAS (Economic Community of West African States) catalogs.