Designing a reconfiguration system for an aircraft requires a good mathematical model of the object. An accurate model describing the aircraft dynamics can be obtained from system identification. In this case, special maneuvers for parameter estimation must be designed, as the reconfiguration algorithm may require to use flight controls separately, even if they usually work in pairs. The simultaneous multi-axis multi-step input design for reconfigurable fixed-wing aircraft system identification is presented in this paper. D-optimality criterion and genetic algorithm were used to design the flight controls deflections. The aircraft model was excited with those inputs and its outputs were recorded. These data were used to estimate stability and control derivatives by using the maximum likelihood principle. Visual match between registered and identified outputs as well as relative standard deviations were used to validate the outcomes. The system was also excited with simultaneous multisine inputs and its stability and control derivatives were estimated with the same approach as earlier in order to assess the multi-step design.