The Spireites have been paired with Wednesday in the second round of the Johnstone's Paint Trophy next month.
Allen left the Owls after a controversial time at Hillsborough, when the club banned some of their own fans from the ground and even took legal action over comments made on supporters' web forums.
He still has money tied up in Hillsborough, and had to have Football League clearance to take over at Chesterfield to make sure there was no clash of interests.
Separated by two divisions at the time, it seemed unlikely the two clubs would meet in the near future, but the JPT draw has paired the two clubs together in what should be a feisty evening at Hillsborough.
Online fans forums are already buzzing about giving Allen a "warm welcome", with some suggestions of a light-hearted repeat of a black balloon protest which was staged against the former chairman during his time in charge of Wednesday.
The tie also sees the return to Wednesday of club legend John Sheridan, who scored the winning goal at Wembley in the 1991 League Cup final win over Manchester United.
Elsewhere in the draw, Huddersfield Town face a tough task when they host Peterborough, while Rotherham United travel to Burton. Bradford City visit Hartlepool.
JOHNSTONE'S PAINT TROPHY - SECOND ROUND DRAW
Northern section (west): Accrington v Stockport, Macclesfield v Crewe, Bury v Shrewsbury, Carlisle v Port Vale.
Northern section (east): Burton v Rotherham, Hartlepool v Bradford, Sheffield Wednesday v Chesterfield, Huddersfield v Peterborough.
Southern section (west): Bristol Rovers v Aldershot, Swindon v Torquay, Cheltenham v Plymouth, Hereford v Exeter.
Southern section (east): Colchester v Wycombe, Leyton Orient v Brentford, MK Dons v Charlton, Barnet v Southend.
Ties to be played week commencing 4 October