Marquis makes his return to Fratton Park as an opposition player on Saturday afternoon following his exit last January.
The 30-year-old first joined Lincoln City on a short-term deal before moving on to the Gas, where he has signed a two-year deal.
Marquis had two spells with Pompey, first as a loan player and then on a permanent basis when he joined for a fee of just under £2m back in the summer of 2019.
Upon his return to a side he had a respectable spell at, Cowley was asked whether Marquis had a point to prove.
‘That’s something you’d have to ask John,” he said with The News.
‘We always found John to be a really good, professional, a really hard working player, who tried incredibly hard here - certainly during the time we were with him.
‘He certainly carries a goal threat at his level and we anticipate seeing the best of John on Saturday.”
Pompey are now pinning their hopes on the additions of Colby Bishop, signed for an expected half a million pounds, as well as Joe Piggott from Ipswich Town.
They can also call on the highly-rated Tottenham Hotspur younger Dane Scarlett, who was wanted by a handful of clubs.
Portsmouth have spent handsomely trying to return to the Championship and Marquis was just one of a few strikers they had hoped would get them out of the division.
During his two-and-a-half seasons, he netted a respectable 36 goals in 121 appearances with his best coming in 2020/21 as they just missed out on the play-offs.
This will not be his first visit back as he returned with Lincoln last season, on that day he was on the losing side, failing to net in a 3-2 defeat.
Cowley added: ‘He’s obviously been back here with Lincoln at the back end of last season and we look forward to seeing John back here on Saturday.
‘I think John has always scored goals at this level.
‘The club paid a significant amount of money for him to score and I think he will always carry a goal threat.
‘Like I said, we’ll always respect his work ethic and we anticipate him being the best version of himself come Saturday.’