Silk fibroin is a promising material for nanocarrier-based drug delivery applications due to its biocompatibility, biodegradability, and mechanical properties, which can be fine-tuned through processing conditions. In this study, we explore the impact of Ca²⁺ and K⁺ inclusion on the morphology of silk nanoparticles and evaluate the short- and long-term stability of silk nanoparticles formed by antisolvent precipitation in deionized water and sodium phosphate buffer. Using advanced electric asymmetric flow field-flow fractionation multiplexed with online detectors (EAF4-UV-MALS-DLS) and orthogonal analytics (DLS, ELS, NTA, FE-SEM), we analyze the physicochemical attributes of silk nanoparticles. We find significant differences in nanoparticle architecture and stability in different buffers, with notable differences in particle size (Rg and Rh), charge, and shape measured over 56 days. Notably, nanoparticles formulated with 0.7 mg Ca²⁺ and 1.1 mg K⁺ maintained superior physicochemical stability, making them promising candidates for nanocarrier-based applications.