To characterize and compare the protein quality of ten durum wheat genotypes grown under three cropping modalities in Algeria (subhumid in Algiers, subhumid-semiarid in Constantine, and semiarid in Sétif), the protein profile of their kernels was performed by High-Performance Liquid Chromatography (SE-HPLC and RP-HPLC). The “variety” factor has a major impact, mainly on the insoluble fraction (Fi), on the gliadin/glutenin ratio, on the large and small glutenin aggregates (F1 and F2, respectively), and on ω-gliadins and high molecular weight albumins (F3). Conversely, the total protein content and the albumin-globulin fraction (F5) depend mainly on the environment. The α- β- and γ-gliadins (F4) are equally dependent on variety and environment. The subhumid-semiarid agroecological conditions of Constantine (SH-SA) favored an important accumulation of proteins (14.1%), particularly by an increased synthesis of omega gliadins and high-molecular-weight glutenin subunits (HMW-GS), compared to those of Algiers (SH) and Sétif (SA). For these latter environments, metabolic-type proteins are predominant, reflected in a higher F5 fraction (p < 0.05) (albumin and globulin), and significantly more alpha-beta and gamma gliadins. The use of chromatographic analyses to characterize wheat genotypes remains a reliable tool for breeding and variety promotion programs and can provide a better understanding of the ecophysiology of cereal crops.