The Portuguese midfielder scored in this week's 2-2 draw at Sunderland.
"Cisco [Junior] has done really well and I said that to him after the game in front of the lads," Stubbs told evertontv.
"He has played well over the last month to six weeks. He's looked more like we expect and so he has been given a pat on the back.
"It has been a difficult time for him, to be fair. He has come in and had to adjust to things, and now his performances have been good. He has to keep doing that to get in and around the first-team squad."