All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
It is permissible for you to put Quran in the mosque with the intention of making it Waqf (endowment). It is not a condition to seek the permission of the administration or the Imaam of the mosque. It was stated in Kashshaaf Al-Qinaa‘ ‘An Matn Al-Iqnaa‘: “Chapter: If the Waqf is not made to benefit a particular person such as making it for the needy people or those who fight in Allaah's Cause or the scholars, or if it is made to benefit entities from whom verbal approval is impossible such as mosques and aqueducts, then Waqf will need no approval from the administrators of mosques and the likes nor is it required to seek approval of anybody else such as the deputy of the Imaam (ruler). That is because if such approval is a condition to make Waqf, then it would be invalid to make Waqf for those entities."
Allaah Knows best.