Isco equalised for Madrid in Sunday's 3-2 victory at home to bottom side Huesca, with the five-goal thriller settled by a Karim Benzema strike in the 89th minute.
The Spain international did not start any La Liga matches under Zidane's predecessor Santiago Solari but has been reintroduced into the fold by the Frenchman.
Solari questioned Isco's commitment and attitude during his brief time in charge of Madrid and Zidane warned the midfielder to keep up his performance levels.
"We all know the player Isco is," Zidane told a post-match news conference.
"I have started him twice, he has scored two goals, so I am happy for him.
"We know the importance Isco has in the squad. Now he must keep training well."
Benzema's 14th La Liga goal of the season ensured he has now found the net against all 34 teams he has ever faced in the competition.
Reports have indicated Madrid will invest heavily in Zidane's squad ahead of the 2019-20 season, with players including Paris Saint-Germain's Kylian Mbappe linked, but the coach feels there will still be a place for his compatriot.
"This year is maybe Karim's best year," Zidane said of the former France forward.
"I will count on him, there are nine games left, and that is the most important, to finish the season well.
"Then we will see what happens, but Karim is a player at this club. I don't believe that will change."