Joey Barton praised his side's battling qualities after they withstood some fierce Guiseley resistance to book their place in the FA Cup third round.
First-half strikes from Paddy Madden and Wes Burns set the League One side on their way to victory before Alex Purver reduced the deficit for the hosts.
But Barton's men had been indebted to keeper Alex Cairns for a pair of early saves which kept the National League North strugglers at bay.
Barton said: "We knew it was going to be a hard game in difficult conditions than we are used to, but you have to navigate these games and do a professional job.
"I thought the lads were outstanding. It was a thoroughly professional performance and certainly late one in the way we managed to close down the Cup tie."
Barton's men started the game knowing the winners would face a third round home tie with League One rivals Wimbledon, who have already claimed a league win at Highbury this season.
But Barton added: "If you can't get a big tie in the draw then the next best thing is to get a home game against a club in your own division.
"It's a nice carrot for both us and Wimbledon to get through and potentially go on and get a big team in the fourth round, and we have got to make sure we rise to that challenge."
Guiseley co-manager Russ O'Neill hailed his side's performance but admitted their excellent start was undone by two mistakes which led to the Fleetwood goals.
O'Neill said: "We're bitterly disappointed because our first half performance was excellent until those two mistakes which cost us dearly.
"In the second half Fleetwood's professionalism told and they closed the game down but I'm pleased with the way we kept fighting.
"The whole cup run has been outstanding and we will now analyse it and really hope to build on it and move on in our league games."
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