Agricultural byproducts such as soybean stover are widely available sources for preparation of nanocellulose, which is an emerging green chemical with versatile applications. In this study, nanocellulose derived from soybean stover, was prepared and characterized as a green stabilizer for oil-in-water emulsions containing antifungal essential oils. Soybean cellulose nanocrystals (CNCs) were produced via alkaline treatment, bleaching, acid hydrolysis, dialysis, and ultrasonication. The as-prepared soybean CNC was characterized by transmission electron microscopy (TEM), zetasizer and rheometer. Droplet size, phase behavior, and thermodynamic stability of CNC stabilized oil-in-water emulsions were investigated. Soybean CNC effectively stabilized oil-in-water emulsions against coalescence but not flocculation. Addition of NaCl reduced creaming index, enhanced the encapsulation efficiency, and freeze–thaw stability of CNC stabilized emulsion. Synergistic effects existed between Tween 80 and salted CNC in stabilizing oil-in-water emulsions. The nanoemulsion stabilized with Tween 80 and salted CNC (with a mean particle size of ~70 nm) demonstrated excellent thermodynamic stability. The nanoencapsulated essential oil had better inhibition activity against the mycelial growth of Aspergillus flavus than pure essential oil. These findings underscore the potential of agricultural byproduct-derived nanocellulose as an eco-friendly nanoemulsion stabilizer with good emulsion thermodynamic stability and improved bioactivity.