The 17-year-old shot 241 in the final of the senior event to claim the gold medal and 243 in the junior category to finish on top of the podium.
In the mixed air pistol final, Manu Bhaker first paired with world number one Russian Artem Chernousov to get the better of the India's Saurabh Chaudhary and Olympic champion Anna Korakaki 17-13.
Manu Bhaker won gold in women's 10m Air Pistol event while Elavenil Valarivan and Divyansh Panwar claimed top spots in women's 10m Air Rifle and men's 10m Air Rifle competitions respectively.
Manu Bhaker won gold in women's 10m air pistol event while Vivaan Kapoor and Manisha Keer won the yellow metal in junior trap mixed event at the Asian Shooting Championships.
Manu Bhaker, who won gold in the mixed team 10m air pistol event in all the four World Cups this year with Saurabh Chaudhary, talked about their partnership and expectations from Tokyo Olympics.
In the air pistol final, the pair of Manu Bhaker and Saurabh Chaudhary prevailed over Yashaswini Singh Deswal and Abhishek Verma 17-15 in a nerve-wracking contest.
The 17-year-old, who is a multiple ISSF World Cup gold medalist, applied under the sports quota and was eligible for direct admission.
Winner of multiple medals at top global events, Bhaker finished third in qualification with a total of 582 points (28 x inner 10s), shooting a solid 98 in her last two rounds.
Manu Bhaker and Saurabh Chaudary won gold in the 10m Air pistol mixed team event in the ISSF Shooting World Cup, claiming India's second gold.
Manu won the women's 10m Air Pistol on day three of competitions while Saurabh bagged a team gold in the men's event.
Their feat came exactly a month after they won the International Shooting Sport Federation (ISSF) World Cup stage gold in the same event in Delhi.
The Indian pair shot a total of 483.5 to finish on top of the podium to finish the tournament with a flourish after a few results that did not go their way over the last three days.
Manu Bhaker finished 14th with 573 in the qualifications while Heena Sidhu was placed 25th with 571.
The 17-year-old Bhaker, owner of multiple ISSF World Cup, Commonwealth and Youth Olympic gold medals, has her eyes trained at a quota for the 2020 Tokyo Olympics.
The initiative by SAI is part of the ongoing efforts of the government to help young athletes balance their sporting career and academics.
Manu Bhaker had earlier tweeted asking Haryana sports minister Anil Vij if she will receive the Rs 2 crore promised to her for winning a gold medal at 2018 Youth Olympics in Buenos Aires.
Former world number one Heena Sidhu, who equalled the women's 10m air pistol qualification world record on Wednesday, finished fourth in the finals.
Youth Olympic Games champions Manu and Saurabh finished with a score of 485.4 in the final, well ahead of the Chinese who managed 477.9.
PM Modi interacted with India's medal winners at the Youth Olympic Games, from where the country returned with 13 medals in its best-ever show at the marquee event.
Manu Bhaker produced a spectacular performance to claim India's first ever gold medal in shooting at the Youth Olympic Games.
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