The spacious and airy central control room at Eggborough contained the control desks for all four units, plus engineering and station services. Each unit had its own control station, wrapping around the corners of the square layout. Engineering and controls for station facilities were placed in the centre.
Between 1996-2000 the control desks at Eggborough were upgraded to incorporate Advanced Plant Management System (APMS) soft desks into the existing Cutlass interfaces. The system enabled the station to move from base load to multishifting in a fast and economical manner. A further upgrade completed in 2011 transferred the controls for the mills, draught and coal delivery to APACS soft desks.