The move was widely criticized, with many suggesting that the only piece of cloth that should be flown outside government buildings is the official flag of the nation.
The swap was first exposed by independent journalist Chris Dacey, who posted a clip to Twitter on Thursday standing in front of Trudeau's office on Wellington Street.
"Guess what is flying here?" he asked. "No Canadian flags at the door of the Prime Minister's office ... We have two Pride flags flying, and no Canadian flags. They Canadian flags have been removed; we don't need Canadian flags any more."
"We have an inclusive flag, it's the Canadian flag," Dacey stated. "I've lived in Ottawa my whole life, and I've never seen the Canadian flags missing off the Prime Minister's office ever. I've never seen another flag put up there either."
When Dacey turned the corner onto Metcalfe Street, however, two Canadian flags could be seen flying proudly near the side entrance. Much like the Liberal government under Trudeau, the Prime Minister's office was deceiving; outwardly preaching one thing while privately practicing another.
In an interview with Dave Rubin, the Post Millennial's Libby Emmons slammed Trudeau for allowing Pride flags to replace the Maple Leaf outside the front doors of his office.
"Canada is all about equity, and Justin Trudeau's ego, and pomp and presentation," she said. "He makes a big point about equity in all of this, but where citizens are concerned, their rights are being curtailed. We know what Justin Trudeau stands for; it is something much more along the lines of authoritarianism."