Finkley Down Farm, in Hampshire, posted a video of the hungry rodents munching on the Christmas dinner accompaniment.
The clip, which garnered 6m views in four days, prompted criticism from some who were concerned the vegetables could cause "fatal" bloating.
However, the farm and the RSPCA and Blue Cross animal charities said they were safe "in moderation".
Facebook user Bob Hammer commented : "These animals are doomed from bloat as a result of being able to eat this many Brussels, Finkley Down Farm you need to be taken to task!!"
Another user, Katie Jacqueline Crossingham, said: "Please be aware: Sprouts can cause bloat in guinea pigs, which can often lead to a nasty, painful death."
The farm, which posted the video as a festive message to its followers, said the welfare of its animals was "paramount" and added it had "expert livestock staff" to deal with the needs of individual animals.
"Here at Finkley we have a large herd of guinea pigs nearly 50 in total - the sprouts in the video are equivalent to one per guinea pig," the farm added.
"We are aware that Brussels sprouts can be difficult for guinea pigs to digest, however, these are safe for them to eat in moderation - something we keep a close eye on to ensure they aren't getting carried away."
An RSPCA spokeswoman described the video as "adorable".
"Sprouts can make a nice Christmas treat for guinea pigs and offering them as occasional treats in moderation can add variety and interest to their diet," she added.
Katie Stiles, animal welfare assistant at Blue Cross, said: "As part of a balanced diet they are absolutely fine.
"Guinea pigs need a mix of vegetables, as sprouts and cabbages can cause bloating - though this is more of an issue with rabbits - but they also need vegetables rich in vitamin C, such as peppers, as they are unable to produce it themselves."

Begonia elachista was discovered at the mouth of a limestone cave in a national park in central Peru.
The park authorities want to build a tourist route to the cave - a move which could threaten the species.
Staff at the botanic garden hope their work will inform conservation efforts for the new species which has been classed as critically endangered.
The Peruvian cave is the only place botanists know that the begonia grows in the wild, but the Royal Botanic Garden Edinburgh (RBGE) said it was "not a safe haven" for the plant as more tourists begin to arrive
RBGE staff are now working with partners in Peru and the US to try to save it.
Peter Moonlight, a tropical biodiversity research scientist at the RBGE, said the begonia did not deserve its reputation as being "repulsively ugly" - as Monty Don once labelled them.
"Many are still poorly understood although they play a critical role in tropical ecosystems and are of great importance as environmental indicator species," he said.
"In many cases they also have a strong role to play in the horticultural sector and as a food source, medicine or other products of benefit.
"The species discovery programme at RBGE gives previous hidden gems - including begonia elachista - a voice on the global conservation stage."

A study for South Lakeland District Council examined details, including types of wagons, the lengths of routes, and the width of streets.
It also took into account how many right turns vehicles made, as these cause them to be delayed at junctions.
The council said the Â£35,000 cost of the research would be offset by savings of Â£40,000 a year.
Changes, which include different collection days for 65% of households, will come into effect in the autumn.
A family farm provoked controversy when it posted a video of guinea pigs eating Brussels sprouts.
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The newest and smallest species of begonia ever found has begun to flower at Edinburgh's Royal Botanic Garden.
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Bin collections in south Cumbria are due to change following a project to "optimise" collection rounds.