The formation of biogenic selenium nanoparticles (SeNPs) through microbial activities is a promising technique that can contribute to the development of reliable, non-toxic and environmentally friendly synthesis methods. Among these, under optimal conditions, myconanotechnology confers particular characteristics due to the generation of bioactive fungal metabolites with various bioactivities. The formed SeNPs are known to be stabilized by the biomolecules of the microorganism, forming a so-called bio-corona or capping structure. The composition of this bio-corona greatly impacts the SeNPs activity, but investigations have been limited to date. The SeNPs produced by Trichoderma sp. have potential applications in crops and environmental management, as both selenium and Trichoderma are known to benefit cultivated plants and phytoremediation. This review summarizes the biosynthesis of SeNPs by Trichoderma sp. and contextualizes the possible correlations between SeNPs and biomolecules produced by Trichoderma; it also provides a missing analysis that could help understand and optimize this process. Biosynthesis methods and probable mechanisms are briefly discussed as well as the role and applications of trichogenic SeNPs as plant protectants, plant biostimulants, and safe biofortifying agents. The knowledge gaps related to mechanisms of trichogenic SeNPs biosynthesis, the control of the desired characteristics for a specific agricultural function, and technology scale-up are discussed in connection with the needed future research directions.