He made his league debut against table-leaders Juventus on 26 January 2020. Lobotka came on as a replacement for Diego Demme, who was booked with a yellow card in the first half. Napoli managed to earn an upset victory over the favourites, by winning 2–1, with goals scored by Piotr Zieliński and Lorenzo Insigne. Cristiano Ronaldo's stoppage time goal did not change the result. He had his first league start in the next round, in a 4–2 away victory at Stadio Luigi Ferraris against Sampdoria. Lobotka played for over an hour and was replaced by Diego Demme, as Napoli led 2–1, after goals by Arkadiusz Milik and Elif Elmas. Demme went on to score the third goal and Dries Mertens sealed the win in stoppage time.