The efficient quantum state reconstruction algorithm described in [P. Six et al., Phys. Rev. A 93, 012109 (2016)] is experimentally implemented on the non-local state of two microwave cavities entangled by a circular Rydberg atom. We use information provided by long sequences of measurements performed by resonant and dispersive probe atoms over time scales involving the system decoherence. Moreover, we benefit from the consolidation, in the same reconstruction, of different measurement protocols providing complementary information. Finally, we obtain realistic error bars for the matrix elements of the reconstructed density operator. These results demonstrate the pertinence and precision of the method, directly applicable to any complex quantum system.