Soybean cellulose nanofibrils (SCNFs) were formed by autoclave-enzymatic hydrolysis combined with ball milling. SCNFs were blended with sodium alginate (SA) to encapsulate lactic acid bacteria (LAB) through inotropic gelation. The effect of SCNFs on the multiscale structure of SA beads, leading to changes in the survival and release of LAB during simulated digestion, was investigated. Microscopy and rheological testing indicated that SCNF10–30 was well-dispersed in the SA paste in the form of interlaced nanofibrils, and could reduce the deformation of the paste under stress by 47.31 %. Multiscale structural analysis indicated SCNF10–30 not only increased the immobilized water of SA beads by 15.59 % by coordinating calcium, but also regulated the in situ-assembly of SA beads, including an increase in the scale of dimers from 6.73 nm to 8.32 nm and improved arrangement, thus forming a dense gel network. LAB viability of SA-SCNF10–30 in simulated digestion was increased by 1.3 log CFU/g compared to SA beads. Cellulose nanofibrils improved gastrointestinal survival and controlled release of LAB better than fiber rods. This study provides a strategy to regulate the multiscale structure of SA beads through nanofibrils to enable stabilization and sustainable release of LAB in gastrointestinal fluids.