FPGA-based reconfigurable systems allow the online adaptation to dynamically changing runtime requirements. However, the reliability of modern FPGAs is threatened by latent defects and aging effects. Hence, it is mandatory to ensure the reliable operation of the FPGA’s reconfigurable fabric. This can be achieved by periodic or on-demand online testing. In this paper, a system-integrated, transparent structural online test method for runtime reconfigurable systems is proposed. The required tests are scheduled like functional workloads, and thorough optimizations of the test overhead reduce the performance impact. The proposed scheme has been implemented on a reconfigurable system. The results demonstrate that thorough testing of the reconfigurable fabric can be achieved at negligible performance impact on the application.