Scannell earned his 100th cap for the province in their 39–22 defeat away to French club Racing 92 in round 5 of the 2019–20 Champions Cup on 12 January 2020, and he captained Munster for the first time in their 2019–20 Pro14 round 12 fixture away to Italian side Zebre on 21 February 2020, though Scannell left the field injured during the first-half of Munster's 28–0 win. A back injury Scannell sustained during training in October 2020 required surgery, ruling him out for two months. He signed a two-year contract extension with the province in February 2021.