The 25-year-old midfielder penned a new deal to stay in the Italian capital until 2026 before the match and arrowed Roma in front three minutes before the break, days after being named in the Azzurri squad for this week's Nations League finals.
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Henrikh Mkhitaryan had Roma two goals in front three minutes later, reacting first after Tammy Abraham's powerful strike had come back off the crossbar, with the hosts able to take their foot off the gas after that and see out the victory with ease.
The result kept Jose Mourinho's side fourth in the standings, six points behind leaders Napoli, while Empoli stayed 10th.