A combination of proton nuclear magnetic resonance (1H NMR) and synchrotron small-angle X-ray scattering (sSAXS) was used to discriminate the speciation and structure evolution of lipolysis products for submicron lipid droplets and lipid loaded in porous silica particles. The free fatty acid (FFA)-to-glyceride ratio was controlled by confining medium-chain length triglycerides (MCT) in porous silica particles, which influenced the colloidal self-assembly structures formed within the lipolysis media. FFA and glycerides released during hydrolysis formed highly geometrically organised structures in a time-dependent manner. Structural transitions from coexisting emulsion droplets and micelles to lamellar structures, and finally to inverse hexagonal phase were observed during the digestion of lipid droplets. In contrast, when hosted in porous silica particles the digestion of lipids resulted in the self-assembly of a lamellar phase that was independent of digestion time. The evolution of structure during lipid digestion was dependent on lipolysis kinetics and the relative concentration of FFA to glycerides, which highlights important implications for the controlled delivery and absorption of lipophilic bioactives.