The local interpretation of microfinite element (μFE) simulations plays a pivotal role for studying bone structure–function relationships such as failure processes and bone remodeling. In the past μFE simulations have been successfully validated on the apparent level, however, at the tissue level validations are sparse and less promising. Furthermore, intratrabecular heterogeneity of the material properties has been shown by experimental studies. We proposed an inverse μFE algorithm that iteratively changes the tissue level Young’s moduli such that the μFE simulation matches the experimental strain measurements. The algorithm is setup as a feedback loop where the modulus is iteratively adapted until the simulated strain matches the experimental strain. The experimental strain of human trabecular bone specimens was calculated from time-lapsed images that were gained by combining mechanical testing and synchrotron radiation microcomputed tomography (SRμCT). The inverse μFE algorithm was able to iterate the heterogeneous distribution of moduli such that the resulting μFE simulations matched artificially generated and experimentally measured strains.