The 31-year-old was forced off the field during Saturday's Aviva Premiership opening 20-15 victory over London Irish.
After having the injury assessed, Monye has confirmed that he has pulled a tendon in his groin and will undergo surgery at the end of the week.
The England international tweeted: "Injuries are so frustrating pulled the tendon of the bone in my groin. So having a op at the end of the wk to get it fixed. 3 months out!
"Thanks for all your get well soon messages too. Always appreciated might get some other work done whilst I'm under the knife #reduction."
Harlequins will face Saracens at the Twickenham Stoop on Friday.