Boothroyd's charges went into the game knowing that a win would seal their place in the UEFA U-21 Championships in 2021 after starting their qualifying campaign with six straight successes.
Andorra, meanwhile, languished bottom of the six-team group, having picked up just a single win over Turkey and a draw with Albania, but the clash proved far more uncomfortable for the visitors than anticipated, and Christian Garcia's late strike sealed a 3-3 tie for Andorra.
The Pyrenean principality's overall record at U-21 level now stands at two wins, eight draws and 47 defeat in 57 games, and Boothroyd was not happy with what he saw from his star-studded England line-up.
He said: “The result is a warning that we have to be bang on every time we play.
“It was a crazy game. Credit to our opponent. We expected to come here and win, but they were strong and direct and put men behind the ball. They were three poor goals to concede and the players are very down. We should have put it to bed. The pitch was a leveller.”
England can nevertheless seal qualification to next year's finals on Tuesday with victory over Turkey at Wolves' Molineux home, and there was some cheer at least for Eddie Nketiah, who equalled the U-21 goal record held by Alan Shearer and Francis Jeffers with his 13th strike in the age group against Andorra.
“Eddie is in esteemed company, isn't he. He took his goal really well, and a great pass from Eberechi Eze to play him in," Boothroyd said of the Arsenal youngster.
“I am really pleased with Eddie. He is the captain of the team when he plays, he is great off the pitch as well as off the pitch, and if he can emulate the guy he now shares the record with he'll have had a brilliant career at the end of it.
“It is just the beginning for him. Hopefully he can play regularly for his club and move on to bigger things with us.”