As the study of the wireless body area sensor network (BASN) keeps growing, corresponding applications such as bio-signal processing for personal healthcare are gaining more attention. To realize a miniature and multi-functional system for biomedical applications, the design of on-sensor mircoprocessor is considered to be a solution. However, how to balance the power consumption and system scalability remains a challenge. In this work, we try to involve the concept of multi-core computing systems into biomedical applications. A fully programmable system architecture based on the proposed two-way pipeline processing unit (two-way PPU) is introduced and evaluated. The proposed two-way PPU is a computing unit that adopts the general purpose processor (GPP) to provide high system programmability, and is easy to be cascaded for system extension. According to the implementation results, the proposed architecture can save up to 91% of energy compared with conventional multi-core architecture in a four-core biomedical processing microsystem.