But, as in Monday's Premier League defeat of Leicester City, Arsenal did not impress in a flat first-half performance.
Although Arsenal are closing in on Europa League qualification, Emery feels there is an obvious area where his team can get better in the weeks to come.
"Each match there is a big opportunity to improve and one is this," Emery told a news conference. "We spoke about it before the match.
"When we were in the dressing room at half-time we spoke and said, 'okay today also, we cannot impose our game in first 45 minutes, but the second half we have the opportunity to change the result and continue in our way, thinking only of winning this match and improving things in the second half'.
"And I think the team did that in the second 45 minutes. But we need to continue finding the solution for the first half to be better.
"The match, for the 90 minutes, there were different things happening tactically and individually.
"The first half is not clear for us, there was not a lot of chances. The second half step by step we imposed our job, our play to win this match."
Emery has regularly spoken of his desire for Arsenal to thrive in the Europa League, a competition he won three years in a row with Sevilla.
And after Welbeck's late impact ensured Arsenal moved clear at the top of Group E, Emery reiterated the value he places on the tournament.
"For us it's very important because we want to finish first in this group," Emery said of the win.
"And at the moment the other club who is with us is Sporting. But also because we want to continue this process. There were many positive things."