The main objective of our studyis to develop a new approach to the annealed proton exchange (APE) method for the fabrication of the multifunctional integrated optical chip (MIOC) used in fiber-optic gyro systems and to eliminate the loss of time and material, especially in mass production applications. In this work, self-polarized waveguides, which are the basic components of a MIOC device, were produced by the APE method and studied. With the developed method, controlled annealing trials have been carried out from a certain region on the LiNbO3 substrate used in waveguide production, and the annealing time specific to the annealing process was determined. By utilizing a special setup for the hot acid process, the proton exchange process was accomplished without a sudden temperature change of the substrate. Using prism coupling measurements of the fabricated waveguides, annealing times were determined to obtain index change values suitable for 45%–50% optical throughput. Mode profiles of devices with high optical throughput that were produced by the proposed method were measured, and it was seen that devices from different proton exchange runs had similar profiles. As a result, many undamaged substrates were fabricated, and their optical quality was found to be within the expected values.