The Indian challenge also ended after the women's doubles pair of Tanisha Crasto and Ashwini Ponnappa lost.
Lakshya Sen's impressive run in the Indonesia Masters Super 500 badminton tournament ended with a quarter-final defeat to Asian Games champion Jonatan Christie, in Jakarta, on Friday.
World No. 12 Sen squandered the advantage of winning the first game and lost 21-15, 10-21, 13-21 to the No. 3-ranked home favourite in 62 minutes.
Later in the day, the new women's doubles pair of Tanisha Crasto and Ashwini Ponnappa lost 13-21, 18-21 to Japan's Yuki Fukushima and Sayaka Hirota in the quarter-finals, bringing down the curtain on India's campaign.
Coming into the match with a 1-0 head-to-head record, Commonwealth Games champion Sen showed his prowess as he opened up a 8-5 lead and maintained it at the break.
Christie knocked off the three-point deficit after resumption and made it 15-15 before the Indian reeled off six straight points to pocket the opening game.
After the change of sides, Sen lost his grip on the match as Christie looked like a different player, zooming to 11-2 in a jiffy before levelling the match.
Christie made a good start in the decider, galloping to a 5-1 lead. Sen took four points on the trot but he was left with too much to do.
The Indonesian ensured there was no hiccups as he marched to a 11-6 lead and maintained a healthy distance from his opponent to eventually seal the contest with a four-point burst.
Sen had reached the second round at India Open last week.