Quantum error correcting code can diagnose potential errors and correct them based on measured outcomes by leveraging syndrome measurement. However, mid-circuit measurement has been technically challenging for early fault-tolerant quantum computers and the readout-induced noise acts as a main contributor to the logical infidelity. We present a different method for syndrome extraction, namely generalized syndrome measurement, that requires only a single-shot measurement on a single ancilla, while the canonical syndrome measurement requires multiple measurements to extract the eigenvalue for each stabilizer generator. As such, we can detect the error in the logical state with minimized readout-induced noise. By adopting our method as a precheck routine for quantum error correcting cycles, we can significantly reduce the readout overhead, the idling time, and the logical error rate during syndrome measurement. We numerically analyze the performance of our protocol using Iceberg code and Steane code under realistic noise parameters based on superconducting hardware and demonstrate the advantage of our protocol in the near-term scenario. As mid-circuit measurements are still error-prone for near-term quantum hardware, our method could boost the applications of early fault-tolerant quantum computing.