During the period of Slobodan Milošević's rule, he was known for maintaining good relations with the independent, anti-Milošević media and for being able to express his party's views on difficult questions.

In June 1999, in the midst of the NATO bombing of Yugoslavia, he announced a humanitarian aid package organised by the party destined for Priština.

[13] Notwithstanding his general support for Milošević in this period, Bajatović ultimately became aligned with a reformist faction in the Socialist Party led by Ivica Dačić.

[19] Soon after his appointment to the assembly, Bajatović indicated that the Socialist Party would not offer parliamentary support to the government of Serbia and Montenegro if Boris Tadić was retained as minister of defence.

Bajatović later threatened that the Socialist Party would withdraw its vital parliamentary support for the government of Serbia under Vojislav Koštunica if extraditions to The Hague continued.

There were rumours that Bajatović would become internal affairs minister, though ultimately this did not happen and party leader Ivica Dačić received the position instead.

[31] The Socialist Party had shifted away from some of its former positions by this time and, specifically, had changed its policy toward the extradition of suspected war criminals; following Dačić's appointment, Bajatović assured the media that the new minister would not threaten relations with tribunal authorities in The Hague.

[32] A report from this period described Bajatović as being on the technocratic wing of the Socialist Party, "favouring personal, economic interests over political ideology."

Bajatović received positions near the top of the Socialist Party's coalition electoral lists in the 2012, 2014, and 2016 elections and was returned to the assembly each time.

[39] After the 2014 election (in which the Progressives won a landslide victory), it was reported that Bajatović urged the Socialists in leave the coalition if they did not receive several important positions.

"[41] He led the Socialist Party's coalition electoral lists in Vojvodina in the 2012 and 2016 elections and served another term in the provincial assembly from 22 June to 4 October 2012.

[44] Bajatović took part in several further deals with Gazprom after this time, and in late 2009 he indicated Serbia's ambition to become a major hub for the distribution of Russian gas in Europe.

Serbia experienced significant fuel shortages in early 2009, when a diplomatic row between Russia and Ukraine hindered the flow of gas to the country.

[49] In late 2009, Bajatović indicated that Srbijagas would seek a concession to construct a pipeline in Bosnia and Hercegovina, with separate sections leading to Sarajevo and Banja Luka.

"[51] Bajatović had an extremely strained relationship with Zorana Mihajlović, a Progressive Party politician who served as Serbia's energy minister from 2012 to 2014.

In June 2015, Serbian prime minister Aleksandar Vučić called on the country to diversify its energy sources and to join an American pipeline operating through Azerbaijan, rather than waiting for Russia to finish the Turkish Stream project.

Bajatović took a different line during the same period, supporting the Russian project and accusing the European Union of obstructing Serbia's energy interests.

[56] In 2014, an anonymous media source indicated that Serbian government could not remove Bajatović from his position even if it wanted to, due to an informal Russian veto.