The songwriter became friends with the One Direction singer after they met at the Brit Awards this year (14).
On Monday (28Jul14), the pair was working on a new track in a studio when they decided to write on Twitter.com about the Middle East conflict.
Both sent "#freePalestine" messages and Malik came under fire from his followers, but the producer - real name Shahid Khan - denies they were taking sides in the conflict and insists they just wanted to make their fans aware of the situation.
Khan tells Bbc's Asian Network radio, "It's about being a humanitarian... We are educated on the subject and the history of Palestine; so we have a responsibility as we are creating an awareness about highlighting children dying... Zayn's biggest fan base is teenage girls so it's good to highlight.
"It's just more about being a human being. If I saw that going on in Israel (I'd do the same), the amount of women and children being killed, that is just too shocking."