A knee ligament injury O'Donoghue sustained in Munster's Pro14 semi-final against Leinster in May 2018 required surgery. He signed a two-year contract extension with Munster in December 2018. O'Donoghue returned from injury in Munster's 19–13 away win against Ospreys in round 16 of the 2018–19 Pro14 on 22 February 2019, and won his 100th cap for the province in their 24–9 defeat against Leinster on 18 May 2019. He captained Munster and won the Man-of-the-Match award in the provinces 18–16 defeat against Edinburgh in round 7 of the 2019–20 Pro14 on 29 November 2019. He signed a two-year contract extension with the province in February 2021.