The increasing demand for life extension of both military and civil aircrafts led to significant advances in repair technology of cracked metallic structures. Consequently, bonded composite repairs of metallic structures became a rapidly growing technology in the field of aerospace. Given the specific characteristics of a bonded composite repair and the differences in the materials used in each case (metal, composite & adhesive), the applicability of a number of Non Destructive Testing methods to trace crack propagation under a composite patch repair of a cracked metallic structure is examined, following mechanical testing in fatigue. In this paper, the main NDT methods examined include the eddy current method applied over a bonded composite repair (i.e. without removing the repair) as well as Bragg grating optical sensors embedded into composite patches. The capability and the reliability of the eddy-current method to detect cracks under a composite obstacle of significant thickness were checked for several patch thickness. The eddy-current method was found to be fully capable of tracing the crack propagation under the composite patch, requiring only proper calibration of the generator. Small differences in the crack lengths between the patched and the unpatched side of the specimen which were examined were explained by their nonsymmetric configuration, which induced different stress intensity factors at the patched and the unpatched sides, as finite element analysis has clearly shown. On the other hand, Bragg grating sensors were proven capable of tracing crack propagation with high accuracy, through interpretation of the differences caused in the strain field over the crack, after comparison with finite element analysis results.