Chiefs have become synonymous with the 3-5-2 system initially employed over the past three seasons under Steve Komphela and it has been retained by Middendorp since his arrival in December.
Former coach Giovanni Solinas initially opted for the traditional back-four, but the system became troublesome as goals constantly leaked through despite the presence of Itumeleng Khune.
After conceding three goals in their CAF Confederation Cup first leg against ZESCO, Amakhosi needed a rapid response in the second leg at home while also maintaining a clean sheet.
However, rather surprisingly, Middendorp opted for a flat back-four at FNB Stadium last Saturday and it seemed to have backfired as the Zambians broke through as early as the 10th minute.
The German then tweaked the line-up at half-time, bringing on 'Dax' Andrianarimanana in place of Leonardo Castro to slot in on the right side of defence, allowing Daniel Cardoso to shift in alongside Mario Booysen and Teenage Hadebe in the centre.
It appeared relatively more solid until an individual error by Willard Katsande midway through the second stanza allowed Jesse Were to slot home unmarked from inside the box.
But Middendorp defended that he was forced to try something different due to the absence of a right-back, with Ramahlwe Mphahlele out injured and Kgotso Moleko omitted from their CAF squad.
"I obviously missed one wing-back, or let's take it from this angle – Moleko can play in the league but he was not registered for the competition [Confederation Cup]," explained Middendorp.
"By the way, I have nothing to do with that [Moleko's omission], he is not registered – that's all I can say. Other players are not registered too, I only have them available in the PSL.
"One criteria or very important principle for us, I think from December 7 and not before, is being flexible tactically and being able to make positional changes.
"I think that's normal in this way to use some ideas and bring into effect. I think of course we were prepared and had certain patterns but 0-1 down after 10 minutes, what are you seeing? You know what's going on – you played the cards in the wrong direction."
Chiefs were ultimately dumped out of the competition with a 5-2 aggregate defeat, falling short of a maiden qualification to the group stages of a continental club tournament.