Wheat, a major food crop, faces significant yield constraints due to losses caused by various diseases, especially rusts and powdery mildew. Since the causal organisms are always evolving, there is a never-ending hunt for new genes/quantitative trait loci (QTLs) for resistance to control the damage. For this purpose, Triticum durum–Aegilops speltoides backcross introgression lines (DS-BILs) developed in our wide hybridization programme were screened against stripe rust and powdery mildew at both seedling and adult plant stages. DS-BILs showed complete to moderate resistance at the adult plant stage while varying resistance and susceptibility at the seedling stage. A total of 1095 single-nucleotide polymorphisms (SNPs) identified on 14 chromosomes of T. durum, using genotyping by sequencing, were used for QTL mapping. Eleven unique QTLs, across six chromosomes (chr1B, chr2A, chr2B, chr3B, chr6B and chr7B) were identified for resistance, four QTLs for field mixture of stripe rust pathotypes, two QTLs for stripe rust pathotype 78S84 and five QTLs for field mixture of powdery mildew pathotypes using stepwise regression-based likelihood ratio test for additive effect of markers and single-marker analysis. Eleven DS-BILs carrying multiple QTLs were identified which will serve as a useful resource to transfer the respective resistance to susceptible cultivars to develop all stage resistant elite cultivars where QTL for stripe rust resistance QYrAs.pau-2A.1 (LOD 3.8, PVE 24.51 linked to SNP S2A_16016633) and QTL for powdery mildew resistance QPmAs.pau-6B (logarithm of the odds (LOD) 3.2, phenotypic variation explained (PVE) 17.75 linked to SNP S6B_26793381) are major targets of the transfer.