The online furore began when Yifang Fruit Tea, a maker of the tea-based drink, closed one of its Hong Kong shops for a day and put up a sign that said in Chinese: "Stand together with Hong Kongers".
Photos of the sign circulated on mainland social media this week, angering users who accused the firm of backing Hong Kong independence. Calls for a boycott spread to other Taiwanese bubble tea brands like Gong Cha, HeyTea, CoCo and A Little Tea.
Yifang and the others were blacklisted by users of China's microblog Weibo. A white list promoted "good" brands.
"Rest assured, I won't spend another cent on you. Yifang is rubbish," a Weibo user named ProfiteroleK wrote in a comment that received more than 1,500 likes.
Hong Kong is facing its worst crisis since returning to China from British rule in 1997, as sometimes violent protests since June against a now-suspended extradition law have become a direct challenge to the city's government and Beijing.
Invented by Taiwan, a self-ruled island considered by Beijing as a renegade province, bubble tea is a flavoured milk tea topped with chewy tapioca balls, also known as pearls.
On the mainland, Weibo posts containing the hashtag "Taiwanese bubble tea shops" were read 350 million times in recent days.
The run-in with Chinese social media users is another example of how companies can get caught in political issues.
In January, Apple and Amazon were called out by a mainland state think-tank for "incorrect" Taiwan and Hong Kong references.
The mainland franchisee of Yifang Fruit Tea said in social media posts the company fired the part-time staff who put up the notice and permanently closed the outlet.
However, Amigo Cheung, the brand manager of the Yifang franchise in Hong Kong, told Reuters by phone that nobody had been dismissed yet and no outlet had been shut.
HeyTea and Gong Cha, on their social media accounts, affirmed their support for "One Country, Two Systems" or "One China", in hopes of distancing themselves from the backlash.
CoCo and A Little Tea could not be reached for comment.
Taiwan President Tsai Ing-wen wrote in a Facebook post this week that "China's political power has invaded into various nonpolitical areas," citing tea as an example.
"For people living in a society with freedom and democracy, we need to stay on high alert for issues like this," Tsai wrote, along with a picture of a cup of ice fruit tea.
Jennie, a mainland student studying at a Hong Kong university, said she had sympathy for protesting students but also felt caught in the middle.
"Seeing the locals around disliking mainland people so much, I fear I'll be driven out (from Hong Kong) by them in the future," she told Reuters.
(Reporting by Beijing newsroom; Additional reporting by Yimou Lee in TAIPEI; Editing by Ryan Woo and Darren Schuettler)