A transmucosal delivery system for oral delivery of one or more biologically active agent associated with an artificial membrane vesicle (AMV), such as a liposome, is provided. The system is especially suited for the delivery of biologically active agents with poor solubility, that are easily degraded in the gastrointestinal tract or that tend to have an unpleasant taste and mouth feel. The delivery system comprises a two-phase system whereby one or more AMV-associated biologically active agents are substantially uniformly dispersed in a semi-solid matrix that allows for maintenance of bioactivity. The dual phase system may further comprise one or more non-AMV associated biologically active agents incorporated within the matrix. Methods of preparing the delivery system and methods of use for delivering biologically active agents to animals, including humans, are also provided.