Campaigners for the Rising Up group, unhappy about a proposed new bus route, have been perched in the trees at Stapleton Allotments for over a month.
"Security specialists" brought in by Bristol City Council started to remove campaigners at about 07:40 GMT but said 20 people still remain at the site.
The council had hoped the process would be over "in a couple of hours".
Protesters chained themselves to diggers, locked themselves to trees using metal pipes covered in concrete and even "dug themselves in" to avoid eviction.
Jennifer Harrison, who has been occupying a tree for 40 days, said she was "not going to walk off site".
"I'm looking down watching people try to physically tug someone along the ground and watching them dismantle our community," she added.
"And watching, yet again, the powers-that-be disregard the wants and desires of the local community.
"I am peacefully occupied, I will not resist in anyway but I'm also not going to walk off site."
BBC Points West's Scott Ellis at the scene:
"I was evicted myself this morning when on site filming.
"I was carried off site along with several protesters including a woman who was completely naked and was left at the gate by the bailiffs.
"There are people up the trees who are singing and have air horns to make as much noise as they can.
"Specialist teams are going up into the trees to get them down. There are also people who have locked themselves on to things and angle-grinders are being used to release them."
A council spokesman said the action followed "several attempts" to resolve the protest and for protesters to leave willingly.
Peter Mann, Bristol City Council's service director for transport, said: "Our top priority is to safely and effectively bring a resolution to this protest.
"We have engaged professional, experienced security experts to help protesters leave the site safely.
"We respect people's right to peaceful and democratic protest but that cannot extend to the illegal occupation of someone else's land.
"Today's actions follow several opportunities for the protesters to leave voluntarily and even today they are being offered the opportunity to leave of their own accord."
Around 20 of the estimated 40 tree-top protesters in Bristol have been evicted by the city council.