Bragg coherent diffractive imaging (BCDI) is a noninvasive microscopy technique that can visualize the morphology and internal lattice deviations of crystals with nanoscale spatial resolution and picometer deformation sensitivity. While BCDI has been successfully applied in various studies of materials, it is less successful for highly strained crystals. Specifically, it is difficult to correctly reconstruct the electron density of a highly strained object using conventional phase retrieval algorithms. Although various algorithms have been developed to overcome this challenge, most of them require a priori knowledge that is not always available in practice. Here we report a phase retrieval workflow that can invert diffraction patterns from multiple Bragg peaks simultaneously. The workflow is explored via simulated diffraction from crystals with various strain conditions. Reconstructions from the workflow consistently demonstrate more accurate electron density maps, in comparison with the conventional method. For highly strained crystals, the workflow improves the reliability and consistency of BCDI phase retrieval significantly.