Michael Lindsay-Hogg was born in New York City in 1940 to Actress Geraldine Fitzgerald. He was educated at Trinity School in New York and at Choate School in Connecticut. For most of his early life, he understood that his father was Fitzgerald's husband, Sir Edward Lindsay-Hogg, to whom she was married until 1946. When Michael Lindsay-Hogg was 16, his mother reluctantly divulged that there had been pervasive rumours that his father was Orson Welles, and she denied them — but in such detail that he was left confused and dubious. Fitzgerald evaded the subject for the rest of her life.

Lindsay-Hogg grew up with a stepfather, American businessman Stuart Scheftel, who married Fitzgerald in 1946.

Lindsay-Hogg began his career in 1965, directing episodes of the British pop programme Ready Steady Go! featuring artists such as the Rolling Stones, the Yardbirds, and the Who. In addition to Ready, Steady,Go!, he directed episodes of Blackmail, The Informer, A Man of Our Times, Half Hour Story, and The Company of Five, a series of television plays. He served as the series Director of The Ronnie Barker Playhouse in 1968. In 1969, an episode of the science fiction anthology Journey to the Unknown that Lindsay-Hogg directed was released as part of a TV movie.

Lindsay-Hogg married Lucy Mary Davies in 1967; they divorced in 1971. Lucy Lindsay-Hogg subsequently became the second wife of the Photographer Antony Armstrong-Jones, 1st Earl of Snowdon in 1978.

Lindsay-Hogg was hired by the Beatles to direct a film. Originally conceived as a television special, Get Back was to feature footage of the Beatles recording a new album and rehearsing for a concert appearance. However, the sessions were extremely acrimonious, and the film and album were shelved for a time following the Beatles' rooftop concert in January 1969. The Beatles returned to the project, and released the newly retitled Let It Be (1970) along with an album of the same name.

For 10 years, in the 1970s, Lindsay-Hogg was romantically involved with British Actress Jean Marsh. He had also been involved with Gloria Vanderbilt, who was the person who finally confirmed Welles' paternity to Lindsay-Hogg.

In addition to his television and film work, Lindsay-Hogg is known for his work in theater. He directed both the original 1978 production (for which he was nominated for a Tony Award) and 1980 revival of Whose Life Is It Anyway?. He also directed Broadway productions of Agnes of God (1982), and The Boys of Winter (1985). Off-Broadway, he helmed Larry Kramer's AIDS drama The Normal Heart in 1985.

Following Let It Be, Lindsay-Hogg continued his work in UK television, directing both episodes and TV movies, including work on the TV serial Brideshead Revisited (1981). His work on the BBC series Play for Today and Play of the Week, and the serial Brideshead Revisited were each nominated for BAFTA awards, in 1974, 1978, and 1983 respectively, with Brideshead Revisited winning for Best Drama Series/Serial. His second feature film, as Director Nasty Habits (1977), is a comedy satire of the Watergate scandal. His third theatrical film, The Sound of Murder, was released in 1982.

Lindsay-Hogg's The Object of Beauty for the BBC's Screen Two series of television films received positive reviews in 1991, and his comedy/drama for HBO, Running Mates, was broadcast in 1992. Frankie Starlight (1995), which followed, was met with mixed reception. In 1994, he directed the Roger Daltrey concert film A Celebration: The Music of Pete Townshend and The Who. The VH1 television movie entitled Two of Us (2000), is a fictionalized account of the last meeting between John Lennon and Paul McCartney. He directed a film adaptation of Samuel Beckett's absurdist play Waiting for Godot (2001).

In 1999, he succeeded to the baronetcy of Rotherfield Hall after the death of his father Sir Edward Lindsay-Hogg, 4th Baronet.

Through his work on Ready Steady Go!, Lindsay-Hogg became acquainted with some of the top rock artists of the day, and was subsequently hired to direct promotional films for their songs. Some of his early promo film work includes videos for the Beatles' "Paperback Writer", "Rain", "Hey Jude", and "Revolution" and the Rolling Stones' "She's a Rainbow", "2000 Light Years From Home", and "Jumpin' Jack Flash". His work on these and other films led Camerimage to award him a retrospective "Music Video Pioneer" award in 2012. The Rolling Stones liked his work, and he was approached in 1968 to direct a full-length television special. Lindsay-Hogg conceived The Rolling Stones Rock and Roll Circus, featuring the Stones and other Musicians playing in a circus atmosphere. The band was not completely satisfied with the result, and the film would not see release until 1996.

His autobiography entitled Luck and Circumstance: A Coming of Age in Hollywood, New York, and Points Beyond was published in 2011. It chronicles his career and his relationship with Orson Welles. After a long hiatus from television and film work, Lindsay-Hogg began directing the television series Tinsel's Town in 2015.