Injectable polymer microsphere‐based stem cell delivery systems have a severe problem that they do not offer a desirable environment for stem cell adhesion, proliferation, and differentiation because it is difficult to entrap a large number of hydrophilic functional protein molecules into the core of hydrophobic polymer microspheres. In this work, soybean lecithin (SL) is applied to entrap hydrophilic bone morphogenic protein‐2 (BMP‐2) into nanoporous poly(lactide‐co‐glycolide) (PLGA)‐based microspheres by a two‐step method: SL/BMP‐2 complexes preparation and PLGA/SL/BMP‐2 microsphere preparation. The measurements of their physicochemical properties show that PLGA/SL/BMP‐2 microspheres had significantly higher BMP‐2 entrapment efficiency and controlled triphasic BMP‐2 release behavior compared with PLGA/BMP‐2 microspheres. Furthermore, the in vitro and in vivo stem cell behaviors on PLGA/SL/BMP‐2 microspheres are analyzed. Compared with PLGA/BMP‐2 microspheres, PLGA/SL/BMP‐2 microspheres have significantly higher in vitro and in vivo stem cell attachment, proliferation, differentiation, and matrix mineralization abilities. Therefore, injectable nanoporous PLGA/SL/BMP‐2 microspheres can be potentially used as a stem cell platform for bone tissue regeneration. In addition, SL can be potentially used to prepare hydrophilic protein‐loaded hydrophobic polymer microspheres with highly entrapped and controlled release of proteins. Soybean lecithin (SL)‐mediated nanoporous poly(lactide‐co‐glycolide) (PLGA) microspheres with highly entrapped and controlled released bone morphogenic protein‐2 (BMP‐2) are developed as a stem cell platform. PLGA/SL/BMP‐2 microspheres have excellent in vitro and in vivo cell attachment, cell proliferation, osteogenic differentiation, and matrix mineralization.