What is the atonement if someone sex with his wife while she was in menstrual?
One must know and understand that having intercourse with one's wife while she is menstruating is forbidden. It would be considered a grave sin to have intercourse with one's wife while she is menstruating as it is evident from the Verse 222 of Chapter 2 of the Holy Qur'an.
Now if someone did have intercourse with their wife while she was menstruating then the very first thing they should do is repent to Allah sincerely and ask for forgiveness. Secondly, they must make firm intention to not repeat the same mistake again to the best of their ability.
Thirdly, if possible, one should give some charity as well as it is the opinion of Imam Ahmad (R.A)
And Allah knows best.
Mufti Ikram ul Haq
Fatwa Center of America