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The biofortification of cereals is a potential solution for increasing Se levels in the human diet. Here we evaluated whether applying selenate and organic N and S sources via foliar alters Se content and species in durum wheat grain. Field trials were conducted in a Mediterranean environment in 2017–2018 and 2018–2019 on old (Cappelli and old Saragolla) and modern (Marco Aurelio and Nadif) durum wheat varieties. Four organic fertilization strategies were evaluated: the control (dry blood meal at sowing), the application of foliar S (Bio-sulphur at flag leaf) and N (liquid blood meal at the beginning of heading), and their combined use in interaction with a foliar application of selenate at the booting stage. The Se content in grain was determined using ICP-MS and its speciation throughout HPLC-ICP-MS and HPLC-ESI-MS/MS. In 2018, the lower rainfall in the ten days before the Se foliar application caused a higher Se accumulation in the grain (1.63 vs. 1.44 mg kg⁻¹ in 2017–2018 and 2018–2019, respectively). A negative effect of organic foliar S on Se content in grain was observed (−24% with respect to the control). The modern Nadif showed the highest Se content (1.87 mg kg⁻¹), followed by the old variety Cappelli (1.57 mg kg⁻¹). Finally, the Se speciation analysis showed the presence of SeMet and SeMetSeCys. The organic fertilization affected only SeMet, with lower values under organic S fertilization and higher values under organic N fertilization.