Separate companies for men and women will be established in the training base's Lahav and Nachshon battalions next month.
These companies will be available for religious soldiers who wish to serve separately, while other soldiers will be able to remain in co-ed companies.
The IDF said the decision is part of a general move to transfer all co-ed battalions—who are entrusted with protecting Israel's borders—to the IDF's Combat Intelligence Collection Corps.
The decision, the IDF stressed, was not affected by recent tensions between religious-Zionist rabbis and the top echelons of the military.
The change is expected to be minor. The IDF's co-ed battalions— Caracal, the Lions of Jordan, Bardelas and the new 47th Battalion—only have a handful of religious soldiers, while there are also very few female cadets in the co-ed companies at the IDF officers' training course.
Eisenkot met with 16 religious-Zionist rabbis for three hours on Wednesday at the Kirya IDF headquarters in Tel Aviv.
The rabbis, who represent the different sects within religious-Zionism, raised issues they've learned about from religious soldiers.
Several of the rabbis described the meeting as good, but complicated.
"I encountered an attentive and open chief of staff, who understands the complexities and the gaps that exist between the orders and the reality on the ground," said Rabbi Meir Nehorai, the chairman of Beit Hillel.
Yossi Yehoshua contributed to this report.
(Translated and edited by Yaara Shalom)