The DEPO will stay in your system for 3 months but you can become pregnant and conceive, before the 3 month time frame is up. One in a 100 women getting a Depo shot every 12 weeks will get pregnant in a year. After stopping it takes on average a further 9-10 months to get pregnant.f you are on depo provera it stays in the system for three months.....you go to take your shot every three months. Going Off Depo. The book Contraceptive Technology says: It is not possible to discontinue Depo Provera immediately.