It is the first documentary to be endorsed by Houston's estate, following her death at the age of 48, in 2012.
"I want audiences to walk out of the cinema and feel positive about Whitney and her music," said Macdonald, who directed The Last King of Scotland.
He said the film would chart Houston's rise from gospel singer to global star.
The film will include interviews with friends, family and collaborators, including Clive Davis, founder and president of Arista Records, who is credited with discovering the singer.
The filmmaking team will also have access to exclusive demo recordings, rare performances and audio archive.
"I want to reveal a woman that even her most die-hard fans never knew; and a woman those new to her life and music will never forget," said Macdonald, whose documentary includes Touching the Void and One Day in September.
"She changed the way pop music was sung - bringing it back full circle to its blues and gospel roots."
"Although we won't shy away from the darker parts of Whitney's life - her descent into addiction - I want audiences to walk out of the cinema and feel positive about Whitney and her music."
Houston was one of the most celebrated female singers of all time, with hits including I Will Always Love You and Saving All My Love For You.
She won two Emmys, six Grammys, and more than 20 American Music Awards, but her later career was overshadowed by drug abuse and her turbulent marriage to singer Bobby Brown.
She was found drowned in a hotel bath in Los Angeles on the eve of the Grammy Awards.
In 2015, Houston's family has heavily criticised a biopic of the star, directed by actress Angela Bassett. The film, which premiered on the Lifetime channel, was made without the family's blessing.
Macdonald's documentary will be released in the UK in 2017.
The life of the late singer Whitney Houston is to be documented in a feature film by British Oscar winner Kevin Macdonald.