As head of Human Resources Stern has overseen a program to convert non-Jewish IDF troops to Judaism. He has also led the integration of hesder units, homogeneous units of Orthodox male soldiers combining yeshiva studies with military service, into mainstream units. While criticised by some religious Israelis that the action was meant only to prevent insubordination of religious troops during the Gaza pullout, Stern maintains that it is better for the troops.
On October 14, 2005, Stern and his family were assaulted in Jerusalem while praying at the Western Wall in protest of his leading role in expelling Jews from the Gaza strip. In 2008 he is said to have "stormed the stage"  to prevent teenage rock star Shira Gavrielov  from performing at a military farewell party on the grounds that she had not served in the military.
Elazar Stern completed his tenure as the head of the Human Resources Directorate in July 2008 and retired from the IDF. He was replaced by Avi Zamir, who received the Aluf rank.