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This study aimed to examine the effect of colloidal structures forming and changing with dispersion and digestion of lipid-based formulation (LBF) on the permeability of exemestane (EXE), a poorly water-soluble drug. Self-nanoemulsifying drug delivery system (SNEDDS), one of the LBF, was developed using Imwitor® 988, Kolliphor® RH 40, and Labrasol® according to the solubility study and optimized using Box-Behnken Design. The EXE-loaded SNEDDS formulation has a 14.46 ± 0.23 nm droplet size with a 0.119 ± 0.053 polydispersity index. EXE was loaded into SNEDDS at 15 mg/g. In vitrodigestion was conducted to investigate the EXE permeability at the digestion medium and the flux of EXE through a dialysis membrane and porcine intestinal tissue was assessed with the permeability step. In vitrodigestion study revealed that the SNEDDS formulation retained the solubilization of EXE and showed moderate supersaturation. The permeation of EXE through the dialysis membrane was observed that the EXE amount on the acceptor side was similar during different digestion phases, but the permeation of EXE through porcine intestinal tissue was slightly different during different digestion phases and EXE permeability was higher at 60 min of digestion although statistically not significant. However, EXE precipitation was observed since the solvation capacity of colloidal structures was slightly decreased at 60 min of digestion. It can be explained by the fact that EXE re-dissolved and increased the free fraction, increasing permeability. This study showed that the drug precipitation in the digestion study does not always result in low permeation and minor differences could be observed more evident in the porcine intestine tissue.