In a magnetic resonance imaging system having a scanner having a magnetic field system, a radio frequency system and a control device, and a method for operating such a system, the control device generates a control signal sequence on the basis of a control protocol for the purpose of executing a number of scan procedures and a number of adjustments for adjusting the magnetic field system and/or the radio frequency system, at least the scan procedures are predetermined by the control protocol. The control protocol furthermore contains a number of local scan transition indicators assigned to the scan procedures, and on the basis of the scan transition indicators, in each case the control device checks to determine if, directly prior to a scan procedure, an adjustment may be applied. The control signal sequence is then automatically generated by the control device such that, if for a scan procedure the necessary adjustment may not be applied prior to that scan procedure, then the relevant adjustment will be executed in advance and/or adjustment parameter values from previously executed existing adjustments will be used.