The Potters, made up primarily of Development Squad players, were dominant for long periods against the non-league outfit but it was first team striker Cameron Jerome who was the star of the night as he grabbed himself a first-half hat-trick.
City started brightly in front of a healthy crowd in Cheshire and they made their early pressure count when experienced striker Jerome opened the scoring with a header with just two minutes on the clock.
The 27-year-old was clearly eager to impress, when minutes later he added his and Stoke's second of the game, when he coolly slotted his shot past Congleton goalkeeper Martin Pearson following a fantastic ball from Tomi Adeloye.
The home side's goalkeeper was certainly kept busy by the Stoke forward line and had to be alert off his line to smother an effort, before tipping another round the post.
City were in complete control and former Queens Park Rangers attacker Peter Skapetis was causing the hosts all sorts of problems with several efforts at goal, as well as striking the bar.
Congleton finally found their feet in the game and almost found a lifeline back into the match on 20 minutes following a speculative bicycle kick from centre back George Whiteoak, which was disallowed for offside.
Skapetis and Jerome then combined again to devastating effect as a great cross from the tricky forward was converted brilliantly by Jerome's left boot to complete his hat-trick inside the opening half an hour.
Whiteoak then went close for the home side but his header was tipped over by Dale Eve, who had been little more than a spectator for the opening third of the encounter.
Oliver Shenton, who less than a month ago signed scholarship forms at the Club, then saw a 25-yard volley thunder against the home side's crossbar before Congleton captain Andrew Langford then had a rare and tame effort at Eve's goal that was easily saved by the Bermudian keeper.
Hat-trick hero Jerome was forced off due to a slight thigh injury as the half drew to a close with Congleton knowing they had to improve in the second half to stop the scoreline from increasing.
Jim Vince's men had the first effort of the second half with an ambitious effort from Scott Sephton which just sailed wide but apart from that one effort, the opening ten minutes was quiet with both sides struggling to create a real opportunity.
Congleton were next to threaten though when a free kick from Jon Paul Hudson forced Eve into a save before Whiteoak struck the follow up wide.
Eve's hands were soon stung moments later after saving low down to his right as Congleton started to apply a period of pressure on the Potters defence.
However, City were to land a sucker punch shortly afterwards when they made it four as Nathan Ricketts-Hopkinson burst down the left hand side before crossing to Skapetis who applied the finish.
Stoke surged forward once more in search of a fifth as a ball was pulled back to left-back Ben Barber who forced Pearson into yet another save.
The Potters then saw James Alabi's late penalty appeal turned down by the referee as the Potters XI made it two wins on the bounce following last weekend's victory over Newcastle Town.
Meanwhile, City's Under-18s secured a 4-2 victory against Wrexham at Clayton Wood on Tuesday afternoon.
Tom Shepherd, Johnville Renee-Pringle, Liam Smith and Julien N'goy were all on the scoresheet for John Perkins' side as they continue their pre-season programme.