There are several existing methods for damage detection based on identifying changes in strain energy mode shapes. Most of these methods require knowing strain energy mode shapes for a structure without damage in order to establish a baseline for damage detection. Usually, the mode shapes from the structure under test should be compared to the baseline mode shapes to identify and locate damage. However, these methods of damage detection are not very suitable for application on structures where baseline mode shapes cannot be readily obtained, for example, structures with preexisting damage. Conventional methods, like building a finite element model of a structure to be used as a baseline might be an expensive and time‐consuming task that can be impossible for complex structures. A new (non‐baseline) method for the extraction of localized changes (damage peaks) from strain energy mode shapes based on Fourier analysis of the strain energy mode shapes has been developed and analytically proved for the cases of a pinned‐pinned and a free‐free beam. The new method looks for characteristic changes in the power spectrum of the strain energy mode shapes in order to locate and identify damage. The analytical results have been confirmed both by the finite element model and impact testing experiments on a free‐free aluminum beam, including single and multiple damage scenarios. This paper presents results of testing the non‐baseline method on a complex structure — Armored Vehicle Launched Bridge, which consists of loosely coupled hinged beams with variable cross‐section. The results of testing confirm applicability of the non‐baseline method to damage detection in complex structures and highlight certain particularities of its use.