Who starts in goal is arguably the toughest shout the head coach has had make as boss, as he needs to decide between Gavin Bazunu and Alex Bass between the sticks.
Then there’s the formation. Does Cowley go with the midfield diamond again or switch back to a 4-2-3-1 formation?
There’s the debate over whether to continue with Arsenal’s Miguel Azeez, rest Louis Thompson and bring back the in-form Joe Morrell into the equation.
Don’t discount the significance of players returning to fitness against the Dons either.
We’ve used our nous and knowledge to come up with what we believe will be the way Cowley goes at Fratton Park tomorrow.
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5. Connor Ogilvie
Warrior's display at Wycombe was his best for Pompey and has been key to the rekindled defensive resolve. Photo: The News
6. Lee Brown
Captain and Mr Dependable has made the left-back slot his own. Photo: The News
7. Shaun Williams
Excellent at Wycombe, but an intriguing selection debate with Joe Morrell returning. Could continue if it's deemed necessary to rest Louis Thompson. Photo: The News
8. Joe Morrell
International duty exertions with Wales, but Cowley is such a fan it's hard to see him leaving out the in-form midfielder. Photo: The News