The mechanical properties of the cellular microenvironment have been shown to critically affect several cell behaviors that are central to embryonic development and disease processes, including cancer. Measuring the mechanical properties that cells perceive in 3D multicellular systems, such as developing embryos or the progression of tumors, has been very challenging. We have developed magnetically responsive microdroplets that enable the application of controlled forces and the measurement of endogenous mechanical properties within developing 3D embryonic tissues and organs, thereby opening new avenues to approach mechanobiology questions in the native environment of cells.