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We develop a protocol for continuous operation of a quantum error correcting code for protection of coherent evolution due to an encoded Hamiltonian against environmental errors, using the three qubit bit flip code and bit flip errors as a canonical example. To detect errors in real time, we filter the output signals from continuous measurement of the error syndrome operators and use a double thresholding protocol for error diagnosis, while correction of errors is done as in the conventional operation. We optimize our continuous operation protocol for evolution under quantum memory and under quantum annealing, by maximizing the fidelity between the target and actual logical states at a specified final time. In the case of quantum memory we show that our continuous operation protocol yields a logical error rate that is slightly larger than the one obtained from using the optimal Wonham filter for error diagnosis. The advantage of our protocol is that it can be simpler to implement. For quantum annealing, we show that our continuous quantum error correction protocol can significantly reduce the final logical state infidelity when the continuous measurements are sufficiently strong relative to the strength of the time-dependent Hamiltonian, and that it can also significantly reduces the run time relative to that of a classical encoding. These results suggest that a continuous implementation is suitable for quantum error correction in the presence of encoded time-dependent Hamiltonians, opening the possibility of many applications in quantum simulation and quantum annealing., Comment: 22 pages, 12 figures