Higher Ground, which was created by the former US president and his wife last year, will “develop, produce and lend their voices” to select podcasts to be made available on the audio app.
Spotify has more than 217 million monthly active users and over 100 million paying subscribers.
Higher Ground already has a partnership with video streaming service Netflix to create a range of documentary and other films.
Mr Obama said: “We’ve always believed in the value of entertaining, thought-provoking conversation.
“It helps us build connections with each other and open ourselves up to new ideas.
“We’re excited about Higher Ground Audio because podcasts offer an extraordinary opportunity to foster productive dialogue, make people smile and make people think, and, hopefully, bring us all a little closer together.”
Release dates and the number of podcasts to be created as part of the multi-year deal have not yet been confirmed.
Mrs Obama said: “We’re thrilled to have the opportunity to amplify voices that are too often ignored or silenced altogether, and through Spotify we can share those stories with the world.
“Our hope is that through compelling, inspirational storytelling, Higher Ground Audio will not only produce engaging podcasts, but help people connect emotionally and open up their minds – and their hearts.”
Spotify’s chief content officer Dawn Ostroff said it was a “privilege” for the firm to work with the Obamas, calling them “two of the world’s most important voices”.
She added: “Connecting people with original and thoughtful creators – especially those with the ability to highlight under-represented and indispensable narratives – is at the core of our mission and we are thrilled that not only will the Obamas be producing content, but that they will be lending their voices to this effort.”