Wrought AZ31 magnesium alloy was used as the experimental material for fluoride conversion coating preparation in Na[BF4] molten salt. Two coating temperatures, 430 °C and 450 °C, and three coating times, 0.5, 2, and 8 h, were used for the coating preparation. A scanning electron microscope and energy-dispersive X-ray spectroscopy were used for an investigation of the surface morphology and the cross-sections of the prepared coatings including chemical composition determination. The corrosion resistance of the prepared specimens was investigated in terms of the potentiodynamic tests, electrochemical impedance spectroscopy and immersion tests in the environment of simulated body fluids at 37 ± 2 °C. The increase in the coating temperature and coating time resulted in higher coatings thicknesses and better corrosion resistance. Higher coating temperature was accompanied by smaller defects uniformly distributed on the coating surface. The defects were most probably created due to the reaction of the AlxMny intermetallic phase with Na[BF4] molten salt and/or with the product of its decomposition, BF3 compound, resulting in the creation of soluble Na3[AlF6] and AlF3 compounds, which were removed from the coating during the removal of the secondary Na[MgF3] layer. The negative influence of the AlxMny intermetallic phase was correlated to the particle size and thus the size of created defects.