One of the limitations of using glued connections in practice is related to the need for connection quality control. Still, the need for the non-destructive quality control of finished products to determine the compliance of the developed structure with the designed one still exists. Considering the small amount of research on timber–concrete composites with glued connections, there is a lack of research on non-destructive methods for the quality control of rigid connections in timber–concrete composite structures. During the literature analysis, no information was found on the possibilities of testing the quality of the rigid timber-to-concrete connection. Therefore, two well-known methods—operational modal analysis and ultrasonic testing—were tested to verify the possibilities of applying these methods in determining defects in the rigid glued connection between the concrete and timber layers in the timber–concrete composite structures. A series of small-scale specimens produced by the stone chips method with and without artificially made defects in the timber-to-concrete adhesive connection was tested by both methods. Operational modal analysis shows significant changes in mode shape, frequency values, and spectral density diagrams. Despite the sufficiently large reflection of the ultrasonic signal on the timber and concrete boundary, the transmitted signal is sufficient to perform local ultrasonic tests for detecting defects in the adhesive connection. Thus, it is concluded that the principles of both methods can be applied in practice, and further research is needed to develop testing technology.