Porous bioceramics have been widely studied for bone tissue engineering. A deep understanding on the mechanism of bone growth and biomineralization depends on the extracted interface information between the new precipitated calcium phosphates (CaPs) and the porous substrate at a nanometer scale. However, due to their intrinsic brittleness and the complexity of the sample shape, there is still lack of such information. Here, by a combination of focused ion beam (FIB) and transmission electron microscopy (TEM), in-situ cross-sectional electron transparent interface was prepared. The precipitated dense apatite layer is composed of individual microgranules which further consist of tiny flake-like crystals. The new crystallites grow along c-axis and are mostly oriented perpendicular to HA substrate. This preferred orientation is more pronounced in the presence of protein. This work offers a novel and feasible approach using FIB-TEM to in situ image porous bioceramic scaffold and precipitated apatite layer interface and can be extended to study many other biointerfaces.