In a method and magnetic resonance apparatus for compensation of contrast inhomogeneities in magnetic resonance images caused by spatial distributions of the radio frequency field associated with the radio frequency pulses that are emitted in order to acquire magnetic resonance (MR) data, multiple individual MR images of a particular region of a subject are recorded with different radio frequency pulse sequences leading to different flip angles. A common contrast-homogenized image for the affected region then is generated based on the different individual images, so that within the contrast-homogenized image, intensity variations due to a distribution of the flip angle are smaller than in the individual images, at least in some areas.