Microencapsulation of multiple drugs and imaging agents is significant for various biomedical applications. In this work we describe a novel method based on flow focusing geometry using tri-axial metallic capillary needles manufactured by a laser beam welding process. The tri-axial needle can be readily cleaned, assembled, and aligned. With this needle assembly, we develop a tri-axial capillary flow focusing device in which different combinations of liquids are focused in the core of a high-speed gas stream coflowing through a small orifice. Under appropriate working conditions, stable cone-jet configurations with three layers of liquids in an external gas stream can be obtained, resulting in multilayered microparticles with outer shell, middle layer, and inner core. The new design of tri-axial needles enables reliable encapsulation of multiple drugs and imaging agents in biodegradable microcapsules with the enhanced size distribution, increased productivity, and improved drug-loading efficiency. Furthermore, in this method the outer and the middle shell fluids can be released to produce monodisperse microparticles at smaller scales which have potential applications in multi-modal imaging, drug delivery, material processing and biomedicine.