Chrysin-loaded phytosomes (CP) were prepared using either soya phosphatidylcholine (SPC) or egg phospholipid (EPL) by the solvent evaporation method. Different phospholipid matrices resulted in significant differences in size, mechanical property and solubility of the CP. The most stable CP was obtained with EPL at a molar ratio of 1:3 (chrysin: EPL, CEP-1:3). CEP-1:3 displayed an average size of 117 nm with uniform size distribution (polydispersity index: 0.30) and zeta potential of −31 mV. A significantly greater elastic modulus of CEP-1:3 (2.7-fold) indicated tighter packing and strong molecular bonding than those of CP prepared with SPC (CSP-1:3). X-ray diffraction and Fourier transform infrared spectroscopic analysis of CEP-1:3 confirmed molecular complexation. CEP-1:3 displayed a greater glucose uptake promoting effect than free chrysin and CSP-1:3 in muscle cells by stimulating gene expression of peroxisome proliferator-activated receptor γ and glucose transporter type 4. The results of the present study suggest that the phospholipid matrix used for the preparation of phytosomes critically influences their performance.