A method for iteratively calibrating a reconstruction kernel for use in accelerated magnetic resonance imaging (MRI) is provided. An MRI system is used to acquire k-space data from multiple slice locations following the application of a multiband radio frequency (RF) excitation pulse. An initial reconstruction kernel is generated from the acquired k-space data, and this initial reconstruction kernel is used to produce an initial image for each of the multiple slice locations by applying the initial reconstruction kernel to the acquired k-space data. The average phase of each slice location is then calculated from these images, and used to shift the phase values of the subsequently acquired k-space data. From the phase-shifted k-space data, an updated reconstruction kernel is then generated. This process is repeated iteratively until a stopping criterion is satisfied.