"I want you to let Spotify know immediately TODAY that I want all my music off their platform," he wrote.
"I am doing this because Spotify is spreading fake information about vaccines, potentially causing death to those who believe the disinformation being spread by them.
"Please act on this immediately today and keep me informed of the time schedule.
"With an estimated 11 million listeners per episode, JRE, which is hosted exclusively by Spotify, is the world's largest podcast and has tremendous influence.
"Spotify has a responsibility to mitigate the spread of misinformation on its platform, though the company presently has no misinformation policy.
Today, about 48 hours after Young issued his ultimatum, Spotify confirmed it would be removing his music from its platform. The company said it regretted the development and hoped to "welcome him back soon".
"We want all the world's music and audio content to be available to Spotify users," it said in a statement.
"With that comes great responsibility in balancing both safety for listeners and freedom for creators. We have detailed content policies in place and we've removed over 20,000 podcast episodes related to Covid-19 since the start of the pandemic."
Young published a new statement on his website in response, thanking his record label for supporting his stance despite the massive revenue hit it will now suffer.
"Spotify represents 60 per cent of the streaming of my music to listeners around the world. Almost every record I have ever released is available – my life's music. [It is] a huge loss for my record company to absorb," he said.
"Yet my friends at Warner Brothers Reprise stood with me, recognising the threat the Covid misinformation on Spotify posed to the world.
"Thank you, Warner Brothers, for standing with me and taking the hit – losing 60 per cent of my worldwide streaming income in the name of truth."
Young stressed that his fans could still find his music on other platforms, including Amazon, Apple and Qobuz.
And he called on other artists to follow his lead.
"I truly want to thank the many, many people who have reached out to me thanking me for taking this position – people who are health professionals on the front lines, people who have lost loved ones to Covid or who are worried for their own children and families. I have never felt so much love coming from so many," said Young.
"I sincerely hope that other artists and record companies will move off the Spotify platform and stop supporting Spotify's deadly misinformation about Covid."
Rogan's show, The Joe Rogan Experience, is among the most popular podcasts in the world. Rogan himself has repeatedly used that platform to cast doubt on the safety and effectiveness of the Covid vaccines, prompting a backlash from health experts.
"If you're like, 21 years old, and you say to me, 'Should I get vaccinated?' I'll go, 'No,'" he said in April of last year, for example.
"If you're a healthy person, and you're exercising all the time, and you're young, and you're eating well, I don't think you need to worry about [Covid]."
To be clear, being young and healthy does not mean you can't be hit hard by Covid, and even die from the disease. As well, young people can be affected by long Covid, the effects of which are still being researched.
Getting vaccinated gives you protection against Covid-19, with the added bonus that you are less likely to spread it to others.
When Rogan's claim was contradicted, including by the White House, he insisted he was "not an anti-vax person".
"I said I believe they're safe and I encourage many people to take them. My parents were vaccinated. I just said that if you're a young, healthy person that you don't need it," he said on an episode of his show.
"I'm not a doctor, I'm a f***ing moron. I'm not a respected source of information.
"But I at least try to be honest about what I'm saying."
Earlier this month, an Australian broadcaster called Rogan out on air as the podcast host overhyped the risk of young boys developing myocarditis as a side effect of the vaccines.
Josh Szeps fact-checked Rogan, pointing out that while there is indeed a low risk of myocarditis happening after vaccination, boys are "about eight times more likely" to develop it as a result of Covid.
"I don't think that's true," Rogan said.
"It is," said Szeps.
The podcast's producers subsequently brought up a New Scientist article that confirmed what Szeps was saying.
When the exchange drew media attention, Rogan magnanimously admitted Szeps had made him "look dumb", while Szeps stressed to his own followers that Rogan "enjoys this kind of pushback".
Also this month, nearly 300 medical professionals signed an open letter urging Spotify to stop "enabling its hosted media to damage public trust in scientific research and sow doubt in the credibility of data-driven guidance".
"Throughout the Covid pandemic, Joe Rogan has repeatedly spread misleading and false claims on his podcast, provoking distrust in science and medicine," the group said.
One of its members, epidemiologist Katrine Wallace, told The Washington Post the experts wanted to "fight against this tidal wave of misinformation" broadcast on Rogan's show.
"I actually think he's a menace to public health, because he speaks on things that have no scientific backing," she said.