Fusarium species threaten wheat crops around the world and cause global losses. The global trend is toward using biological materials such as selenium (Se) in nano form to control these fungi. Bulk selenium is toxic and harmful at high doses; however, selenium nanoparticles are safe; therefore, the aim of this study to employ the biological selenium nanoparticles (BioSeNPs) synthesized by Lactobacillus acidophilus ML14 in controlling wheat crown and root rot diseases (CRDs) induced by Fusarium spp., especially Fusarium culmorum and Fusarium graminearum, and their reflection on the growth and productivity of wheat. The ability of BioSeNPs to suppress the development and propagation of F. culmorum and F. graminearum and the CRDs incidence were also investigated. The obtained BioSeNPs were spherical with a size of 46 nm and a net charge of –23.48. The BioSeNPs significantly scavenged 88 and 92% of DPPH_and ABTS_ radicals and successfully inhibited the fungal growth in the range of 20–40 mg/mL; these biological activities were related to the small size of BioSeNPs and the phenolic content in their suspension. Under greenhouse conditions, the wheat supplemented with BioSeNPs (100 mg/mL) was significantly reduced the incidence of CRDs by 75% and considerably enhanced plant growth, grain quantity and quality by 5–40%. Also, photosynthetic pigments and gas exchange parameters were significantly increased as compared to chemical selenium nanoparticles (Che-SeNPs) and control. This study results could be recommended the use of BioSeNPs (100 mg/mL) in reducing CRDs incidence and severity in wheat plants, enhancing their tolerance with drought and heat stress, and increasing their growth and productivity as compared to control and Che-SeNPs.