There were Jain temples in Fatehpur Sikri, most probably Built by Kacchwaha & Sikarwar Rajputs. Former Director ASI, Dr. DV Sharma carried out extensive research & brought out that Fatehpur Sikri was actually Vijaypur Sikri ruled by Sikarwar Rajput king Dhamdev Singh.
Interestingly Badayuni and Abul Fazal, both have written that Vijaypur/Fatehpur Sikri was founded by Akbar, but architectural and literary evidence contradicts their claims. Even Babur mentions this place as Sikri in his memoirs. Sikri was under the direct lordship of Sikarwar Rajputs(Subclan of Pratihars) before the Mughals. Sikarwars fought alongside Rana Sanga in the battle of Khanwa (19 km from Vijaypur Sikri). Later on, the same clan & its members migrated to Gehmar Village in Gazhipur & Chainpur, etc.
Apart from Jain, the settlement patterns signify the presence of Vaishnav, Saiva & Shakta temples in Vijaypur Sikri. However, the Sanskrit Inscription found with Jain Sculptures(1010AD), tells us that before Sikarwars, the area was under the sovereignty of the Kacchapghata Rajput Dynasty.