The permeation of amino acids and di-peptides with different hydrophobicities across the oil phase in W/O/W double emulsions was investigated at different concentrations, considering the pH of the aqueous phase. Moreover, the particle size, yield of entrapped water and release kinetics of the double emulsions was evaluated as a function of time. Regarding the release of the entrapped amino acids and di-peptides, their hydrophobicity and the pH had a significant effect, whereas the concentration of the dissolved compound did not lead to different release kinetics. The release of the amino acids and di-peptides was faster at neutral pH as compared to acidic pH values due to the increased solute solubility in the oil phase for more hydrophobic molecules at neutral pH. Regarding the effect of the type of oil, much faster amino acid transport was observed through MCT oil as compared to LCT oil, which might be due to its higher solubility and/or higher diffusivity. As di-peptides released faster than amino acids, it follows that the increased solubility overruled the effect from the decreased diffusion coefficient of the dissolved compound in the oil phase.