The description of the complex separability structure of quantum states in terms of partially ordered sets has been recently put forward. In this work, we address the question of how to efficiently determine these structures for unknown states. We propose an experimentally accessible and scalable iterative methodology that identifies, on solid statistical grounds, sufficient conditions for non-separability with respect to certain partitions. In addition, we propose an algorithm to determine the minimal partitions (those that do not admit further splitting) consistent with the experimental observations. We test our methodology experimentally on a 20-qubit IBM quantum computer by inferring the structure of the 4-qubit Smolin and an 8-qubit W states. In the first case, our results reveal that, while the fidelity of the state is low, it nevertheless exhibits the partitioning structure expected from the theory. In the case of the W state, we obtain very disparate results in different runs on the device, which range from non-separable states to very fragmented minimal partitions with little entanglement in the system. Furthermore, our work demonstrates the applicability of informationally complete POVM measurements for practical purposes on current NISQ devices.