The complex bone marrow microenvironment or niche is an important anatomical structure responsible for hematopoiesis and providing support to the immune cells function. Being the source of immune and blood cells, the interaction of these hematopoietic stem and progenitor cells with the cellular niches regulates their ability for self-renewal, proliferation, and differentiation. Dynamic imaging not only provides spatiotemporal information of cell motility but also the morphological changes due to cell-cell interactions in the bone marrow, providing insights into the ongoing physiological activities within the tissue. Here, we describe customized stages with compatible equipment best suited for the upright two-photon microscope, accompanied by detailed methods for both calvarial and tibial intravital imaging. We demonstrate a general protocol for calvarial imaging using a minimally invasive surgical approach, and introduce a bone shaving-based tibial imaging as a complementary method. To demonstrate the applicability of our method we used Lyz2-EGFP transgenic mice to track bone marrow neutrophil activities as an example.