The 26-year-old left the Emirates Stadium for West Ham United earlier in June after learning that his first-team opportunities at Arsenal would be limited under the new manager.
Speaking to Sky Sports News, Emery stated that he would prefer to keep his talks with Wilshere private, but explained his unwillingness to assure the midfielder of a starting berth.
"The conversation with Wilshere was a very good conversation," said the Spaniard. "I explained to him my opinion and how I will want to create the team and not sure [I could] say to him he's going to play in the XI.
"Also he explained to me the decision is not easy for him but he wanted to choose the best option for him. Every time it was with respect.
"I know this player is very important for the supporters, he grew up here with Arsenal. But I don't give for him one post in the starting XI. It's for that he chose to leave here and I respect this."
Wilshere also missed out on a place in Gareth Southgate's England squad for the World Cup despite making 38 appearances in all competitions last season.