Homogenization is a numerical technique to obtain the equivalent mediated response of a complex material. However, there are some scenarios in which the complexity of the physical phenomena present in the real structure makes it difficult to generate a faithful Representative Volume Element (RVE). In these cases, it may turn easier and more reliable to perform a homogenization directly by experimental test results. For this reason, we present a procedure to build-up the whole stiffness matrix starting from experiments. This approach is here discussed to get a homogenised two-node beam element. The procedure requires some flexibility measurements, thus allowing fewer measurements if compared to stiffness-based approach. The method is verified with some experiments carried on a frame structure. The comparisons with a Finite Element model build up with stiffness matrix assembly demonstrates the validity and robustness of the proposed procedure.