The correlation between microstructure, rheology, and tribological behavior in silica-based nanofluids dispersed in vegetable oils was investigated. Nanofluids containing 3 vol.% hydrophilic silica in coconut oil (CO), CO with 10 vol.% of Taladrine (CO-10Tal) and the 50CO-50SO mixture of CO and sunflower oil (SO) were characterized using tribometry, rheometry, and thermal analysis. Friction-velocity curves revealed two lubrication regimes, boundary and mixed lubrication, which were interpreted using a semi-logarithmic model. The slope parameter was identified as a measure of shear-induced activation of lubrication mechanisms. Results showed that lubrication mechanisms evolved from tribofilm-dominated behavior with particle-assisted sliding to mobility-controlled regimes involving rolling and dynamic third-body layers. Rheological measurements indicated the fragmentation and restructuring of fractal aggregates. The intrinsic viscosity and maximum packing fraction provided quantitative descriptors of aggregate structure. The CO-10Tal nanofluid exhibited large, open aggregates with high intrinsic viscosity and strong shear sensitivity, resulting in higher friction at low velocity and rapid friction reduction at bigger velocities. The 50CO-50SO colloid displayed compact aggregates, enhanced dispersion, and superior tribological performance due to increased particle mobility. The results demonstrated that shear-induced microstructural evolution controlled frictional behavior. This work provided a unified framework linking aggregation, rheology, and nanolubrication mechanisms in bio-based systems.