President of Apulia
On 31 May, Emiliano won the 2015 Apulian regional election with more than 47% of votes, doubling the votes of the second candidate, Antonella Laricchia, of the Five Star Movement (M5S).
In September 2016, Emiliano signed with the Prime Minister Matteo Renzi the so-called "Pact for Apulia" in order to release 2.7 billion euros from the Fund for Development and Cohesion (FSC) to be assigned to Apulia region for various investments in the territory. Among the social policies promoted, there was the Regional Income of Dignity, a guaranteed minimum income for indigents.
Despite the sign of the Pact for Apulia, Emiliano often criticized Prime Minister Renzi, who was also the leader of his own party, who was considered by Emiliano too centrist. He often implemented regional policies in contrast with those of the government. This contrast reached its peak at the 2016 Italian oil drilling referendum, which was promoted and supported by Emiliano and opposed by Renzi. During the referendum campaign, Emiliano repeatedly accused the government of having introduced the law to favor oil companies and Renzi accused the governor of having promoted the referendum only for personal purposes. Although 86% voted in favour of repealing the law, the turnout of 31% was below the majority threshold required to validate the result. Moreover, during the campaign for the 2016 Italian constitutional referendum, concerning the Renzi's Senate reform, Emiliano supported the "No", in open opposition to the line of his party. On 4 December, "No" won with 59% of votes and Renzi resigned as Prime Minister.
On 21 February 2017, Emiliano announced his candidacy in 2017 PD leadership election, scheduled in April, where he would challenge Renzi. On 10 March, Emiliano presented his electoral programme with the slogans "We Are Party" (Noi siamo partito) and "Italy Is Our Party" (L'Italia è il nostro partito). He described his candidacy as a revolution, and stated that he wanted a party closer to the people, especially the poorest, accusing Renzi of drastically changing the PD and of abandoning people on low incomes. He also accused Andrea Orlando, the other candidate who was Justice Minister also in Renzi's government, of supporting Renzi's liberal and centrist policies, and not to have ever opposed his reforms. Emiliano also added that he would not run to become Prime Minister, as Renzi did from February 2014 to December 2016. Emiliano asked for the M5S, Article One (Art.1), Progressive Camp, and Italian Left (SI) supporters to vote for him to beat Renzi; his intention is to build a centre-left to left-wing alliance composed of PD, Art.1, and SI, which can cooperate with the M5S. Despite Emiliano's strong support in the poorer South, Renzi was elected by a landslide, receiving 69% of votes, against 20% of Orlando, and 11% of Emiliano.
On 3 December 2018, following the Constitutional Court of Italy's judgement that magistrates are ineligible for party membership, Emiliano announced that he would be resigning from the party.
In the run-up of the 2020 regional election, on 12 January 2020, the PD held its primaries, which Emiliano won. Following the primaries' victory of Emiliano, considered by Italia Viva (IV) too close to the political positions of the Five Star Movement (M5S), Renzi announced that his party would run separately from the centre-left coalition. During the electoral campaign, Emiliano launched his own civic list "Con Emiliano" (English: "With Emiliano"). On 25 September, Emiliano was confirmed president of the region, gaining 46.8% of votes and defeating the centre-right candidate Raffaele Fitto with 38.9%.