The 42-year-old admits he thought the defender would have left the club earlier this summer and is eager to bolster his options after the defeat to Real Madrid
Emery's men lost the Uefa Super Cup clash to La Liga rivals Real Madrid 2-0 in Cardiff on Tuesday, courtesy of a Cristiano Ronaldo double.
The Europa League champions missed Moreno - according to Emery - with the Spanish left-back absent from the trophy play-off as he finalised a deal with the Premier League club.
While Emery said Moreno's exit had been likely throughout the close-season, the 22-year-old's absence from their clash with powerhouses Real was costly.
"The offer has been on the table for a month and a half to two months. I saw him leaving the club earlier than I saw right now, but its unfolded today [Tuesday]," Emery said after the match.
"We knew they were following him in England, the teams who were interested and that the meetings were advancing. We were prepared to lose Alberto.
"Unfortunately, we were counting on him being here with us today, but Fernando Navarro put in a great performance.
"We're looking for another good player to join us, who can help complete our objectives."
Sevilla were underdogs against the Champions League winners given the latter's star power, but the loss was no easier to take for Emery - who claimed his side performed admirably at the back.
"Clearly, you play to win the finals. We all came into this match on a single mission," the former Valencia boss said.
"We played to our strengths but then comes the time when you must allow those options to play out and make them happen. Positionally, we defended well.
"We lacked precision in front of goal in the counter-attack, we need to refine that. The difference was in the counterattack, even though we allowed very few of them, they were successful."