February's ruling in favour of the National Gay and Lesbian Human Rights Commission (NGLHRC) reversed a ban imposed on it by the national board that regulates NGOs, and was welcomed by the commission as a minor affirmation of LGBTQ Kenyans' place in society.
But, in a country where same-sex acts remain punishable by up to 14 years in prison, the ruling has also led to a menacing backlash.
President William Ruto said that, while he respected the supreme court's decision, "it doesn't mean we have to agree with it" - a reaction less hostile than from many other leading politicians.
Meanwhile, NGLHRC activists have reported a surge in threats against the community. Calls it has received reporting abuse, including assaults, threats and discrimination, rose from 78 in January to 117 in February and 367 in March, the commission said.
Victims include a 31-year-old lesbian who was on the back of a motorbike taxi on the capital Nairobi's outskirts last week when she was stopped by about 10 motorcycle riders.
They surrounded her, pushed her, and shouted they knew she was "one of them" - meaning gay - before a couple walking past intervened and the crowd dispersed, the woman, who asked not to be named, told Reuters.
"Things have gotten worse after the ruling and Uganda's recent introduction of the Anti-Homosexuality Bill," she said, referring to a draft law passed by neighbouring Uganda's parliament last month that would criminalise identifying as LGBTQ and introduce the death penalty for some same-sex acts.
For now, Kenya is still seen as a relative haven for LGBTQ people in a hostile region. Unlike in many of the more than 30 other African countries where same-sex relations are illegal, its colonial-era anti-gay law is rarely enforced.
The court's judgment said the NGO board's ban on NGLHRC violated constitutional freedoms of association and protections against discrimination.
Yet the NGLHRC's records shows that discrimination - by employers, landlords and healthcare providers - is on the rise, and one lawmaker has threatened to introduce a bill imposing a life sentence for homosexual acts.
For Kevin Mwachiro, an LGBTQ activist for 15 years, this is the most challenging time that the community inside Kenya has experienced.
"People... feel like they have the right to attack you. And they feel that they have that right because of what has been said in the press, what the government has said," he said.
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