The livewire striker struck first in the 21st minute when he latched on to a Jordan Rhodes through ball and shrugged off two challenges before slipping the ball under City keeper John Danby.
McDonald made it two 10 minutes before the break when he got on the end of a Sam Wood pass and squeezed a low drive home from a tight angle.
The Bees’ leading scorer made it three on the stroke of half-time. Rhodes was fouled in the box by Chester defender Anthony Barry and McDonald stepped up to fire the resulting spot-kick into the roof of the net.
Rhodes could have made it four midway through the second half but flashed his shot just wide.