Abbington was the partner of British actor Martin Freeman, whom she met on the set of the film Men Only in 2000. The couple appeared together on screen in productions such as The Debt, The Robinsons, The Good Night and Sherlock. They lived in Hertfordshire before announcing their separation in 2016. Abbington and Freeman have two children.

She appeared in the TV series The Bill until 2007 playing various characters. During that time she also appeared in the TV series Wycliffe, Casualty, Dream Team, The Sins, Shades, Doc Martin, Coupling, and Teachers. She appeared in the 2005 comedy sketch show Man Stroke Woman and the 2007–2008 comedy After You’ve Gone with Nicholas Lyndhurst. She has also appeared in recurring series such as Bernard’s Watch and Case Histories.

In 2013, she began appearing in the television series Mr Selfridge as Miss Mardle alongside Jeremy Piven and Frances O’Connor. In 2014, Abbington appeared in the third series of Sherlock as Mary Morstan, the wife of John Watson, played by her then real-life partner Martin Freeman. In 2015 she appeared in the BBC TV series Cuffs.

On stage Abbington appeared in August 2018 in the role of Annette in God of Carnage at the Theatre Royal, Bath, and in 2019 as the character Anne in Florian Zeller’s play The Son at the Kiln Theatre in Kilburn, London which later that year transferred to The Duke of York’s Theatre in London’s West End.