The present work anticipated crystallinity-tuned silk fibroin (SFIB)-sodium alginate floating microbeads (MB) as a candidate for nevirapine (NEV) sustained release. Briefly, crystallinity tuning was accomplished using solvent annealing. The changes in structural conformation of SFIB were validated using FTIR spectroscopy. Here, the tangent baseline method revealed changes in crystallinity of floating NEV-loaded SFIB-MB. Importantly, solvent annealing offers conversion of amorphous ‘α-helix’ to crystalline ‘β-sheet’ of SFIB, helping to modify drug release from the matrix of SFIB-sodium alginate. As well, NEV-loaded SFIB-MB demonstrated good floating profile. The NEV-loaded SFIB-MB with ethanol (ETH-6) annealing for 6 hours shows 25.853% drug release at 12 hours (pH = 1.2), compared to untreated NEV-loaded SFIB-MB (65.132%, 12 hours, log p < 0.0001). The release kinetics of batch ETH-6 revealed first-order release kinetics and Fickian diffusion (n = 0.468) was found to be the drug diffusion mechanism. Therefore, crystallinity-modified floating NEV-loaded SFIB-based MB will open a new door for modified drug delivery.