A senior Israeli air force official stated, "the aircraft will be designated F-35I, as there will be unique Israeli features installed in them." The United States initially refused to allow the integration of Israel's own electronic warfare systems into the aircraft’s built-in electronic suite. However, Israel planned the introduction of a plug-and-play feature added to the main computer to allow for the use of Israeli electronics in an add-on fashion, and to fit its own external jamming pod. The IAF dispatched two officers to the US where they discussed issues involving the integration of Israeli technology into the fighter with Pentagon and Lockheed Martin officials.

In July 2011, it was reported that the U.S. had agreed to allow Israel to install its own electronic warfare systems and missiles in its F-35s in the future. In 2012 Lockheed was awarded a contract to make changes to the first Israeli F-35s to allow the installation of Israeli electronic warfare equipment produced by Elbit Systems. This equipment will use "specific apertures... in the lower fuselage and leading edge". Israel also plans to install its own indigenously-produced guided bombs and air-to-air missiles in the F-35's internal weapon bays.