The 21-year-old Nigeria international played 90 minutes during Arsenal's 2-1 defeat at Manchester United in the Premier League on Sunday but Wenger said after the match Iwobi was struggling with a hamstring injury.
"I believe it is very good. I am still being assessed but to me it is good and I will be okay," Iwobi told Sky Sports.
"We will have to wait and see but I believe I will be okay and fit (for Atletico)."
The north London club need a win at Atletico's Wanda Metropolitano stadium to reach the final after the two teams played out a 1-1 draw at the Emirates last week.
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