The Prodigy vocalist was found dead at his home in Essex on Monday morning.
Police said his death was not suspicious.
Flint, who was 49, competed in the 5km Chelmsford Central parkrun on Saturday, posting a personal best time of 21min 22sec.
Writing on their website, organisers described Flint as “one of our newer runners”, adding: “We wished he could have been part of our parkrun community for longer than he was.
“Our condolences and thoughts go to his family and friends at this sad time.”
Flint was a tour de force in the British rave music scene in the 1990s, known for his bright green spiky hair, facial piercings and energetic, manic stage performances.
He rose to fame as part of Brit Award-winning electronic band The Prodigy, loved by fans for their hits including Firestarter and Breathe as well as their anti-establishment stance and fusion of techno, breakbeat and acid house.
They released their latest album No Tourists in November, their seventh consecutive number one record.
On Monday afternoon, a bouquet of purple flowers was laid by the gate next to Flint’s home, which is located down a rural track and hidden behind wooden gates.
Flint’s Grade II-listed five-bedroom house was listed on property website Rightmove as having had a sale price of £1.9 million in March 2017.
The website says the property has period features, a cellar, a Victorian Hartley Botanic Greenhouse, an outdoor pool and pool house and an all-weather tennis court, and that it is sprawled over “approximately six acres of land”.
Following his death, tributes were paid from around the entertainment industry.
Bandmates Liam Howlett and Maxim described Flint as “a true pioneer, innovator and legend”.
They said Flint was their “brother and best friend” and that “he will be forever missed”.
In a separate post, Howlett claimed that “our brother Keith took his own life over the weekend”.
Gail Porter, who dated Flint between 1999 and 2000, was among those to comment.
The presenter wrote the word “heartbroken” on Twitter. James Blunt penned an emotional tribute to Flint, saying he showed him kindness when others in the industry did not.
The singer wrote on Twitter: “At the Q Awards years ago, when @NoelGallagher was saying he was leaving Ibiza because I’d moved there, and @DamonAlbarn refused to be in the same picture as me, and @PaulWellerHQ was saying he’d rather eat his own s*** than work with me, Keith Flint came over, gave me a hug, and said how thrilled he was for my success.
“Keith, I only met you once, but I shed a tear at the news of your death. In our business, there are no prizes for being kind, but if there was, that Grammy would be yours.”
In a lengthy Instagram post, Queen’s Brian May shared a story about a backstage meeting with Flint, whom he had assumed would “hate us”.
However, May said: “So I just nodded in respect when I saw him at the other side of the stage while the gear was being changed over.
“He ran straight over and did that Wayne’s World tongue in cheek bowing thing, and then spent a good five minutes telling me very warmly how much he loved our music and had been inspired by it in his life.
“After that, I perceived him very differently. And I enjoyed their records even more. But that’s the only conversation we ever had.”
Electronic music artists Chase And Status and The Chemical Brothers, who are both considered pioneers in the big beat genre along with The Prodigy, were among those sharing tributes for Flint.
Essex Police, who were called to Flint’s home on Monday morning, said a 49-year-old man had been found dead and the death was not being treated as suspicious.