The midfielder was left on the bench as Madrid sealed a 3-1 victory over their La Liga rivals at Camp Nou.
Isco has started just two matches this season and it appears the 28-year-old is less than happy with the amount of playing time he has received under Zidane.
As he took his place on the bench at Camp Nou on Saturday, a conversation between Isco, Luka Modric and Marcelo was caught by Spanish television station Movistar.
Isco told his two Madrid teammates: ‘If he has to take me off, it’s in the 50th or 60th minute of the game.
‘Sometimes at half time. If he has to bring me on, it’s in the 80th minute.’
Zidane’s side had entered the game off the back of two defeats to Cadiz in La Liga and Shakhtar Donetsk in their Champions League group-stage opener.
Madrid are next in action on Tuesday evening as they travel to Germany to face Borussia Monchengladbach in the Champions League.