Moffat wrote the historical drama The Village, depicting life in a Derbyshire village through the eyes of a central character, Bert Middleton. The first series, covering the years 1914 to 1920 in six episodes, premiered on BBC1 in 2013, and a second and final series, set in the 1920s, was made in 2014. Moffat envisions more series totalling up to 42 episodes that will continue the story through the 20th century. The proposed project is similar to the German film series Heimat, written and directed by Edgar Reitz, which told the story of a German family from 1919 to 2000.

His first play was called Fine and Private Place and was broadcast on BBC Radio in 1997. His best-known plays are Nabokov's Gloves and Iona Rain.

Moffat won the Writer's Award from the Broadcasting Press Guild for North Square, and was nominated for a BAFTA Award in 2004 for writing Hawking, a TV drama about the scientist Stephen Hawking. In 2009, he was awarded two BAFTAs for Criminal Justice, one for Best Television Drama Serial and one for Best Craft Writer.

The BBC broadcast Moffat's drama series Undercover in 2016. Moffat took inspiration for the fictional drama from real-life revelations about British police officers who had formed long-term relationships with Activists they were investigating while undercover, as well as from the London Metropolitan Police Service's secret surveillance of the family of murdered teenager Stephen Lawrence.