The summer signing has underwhelmed supporters this season after a huge £38million summer move, and is yet to register a single goal – and has just one assist – in Wolves colours.
Nunes has shown glimpses of his quality under Lopetegeui, but has found himself on the bench in the last two games, and the head coach wants more from the Portugal international.
When asked about his lack of an impact this season, Lopetegui said: "It's not easy to make the difference in the Premier League. It's not easy for anyone.
"He's a good player and he has to improve, as do the rest of the players.
"He has a good physical condition and needs to improve on other things. He knows.
"But we are helping him to try to improve and to become a better player.
"Matheus is a very good player who has physical strengths and quality.
"He has to improve a lot of things, as do the rest of the players, but he's trying and working very hard.
"He's young, but in the same way he's played a lot with us and I think he's going to be a key player for us in the next matches."
Nunes' best moments have come when he has space to drive forward from midfield, after starting in a deeper position.
Lopetegui started him there when he first arrived at Wolves, before moving Nunes to an adapted left wing role.
"All the players have different things to improve, always," Lopetegui added:
"If they want to become better players, they have to improve in a lot of facets, this is normal.
"It's his first season here in England and it's not easy to play here. The rhythm here is different to other countries.
"You have to adapt your qualities and strengths to this rhythm and he's trying to do that.
"He's a midfielder of course, he has played inside and on one wing going inside because he has the quality to do it. He has pace.
"We try to help him to take advantage of his strengths."