Assalamu ‘Alaykum Wa Rahamtullah.

Zakah will not be valid if it is paid directly to the Masjid or Madrasah (Religious Institution). One has to make a poor person the owner of the goods/wealth otherwise Zakah will not be valid.

It is in Bahar-e-Shari’ah:

“There are many people who send their Zakat money to poor Madrasah, they should make sure that they tell the trustees of the Madrasah that this money is Zakat money, so that the Trustees can keep the money separate and spend it on the poor children who are studying, otherwise if they are unaware then they may spend the money on other causes, whereby the Zakat will not be fulfilled.” 

In order for the Masajid or Madaris to use Zakah money, the money should be given to the poor, who in turn can give it to the Masjid by his one will. 

Also in Bahar-e-Shari’ah it states:
“…When the Faqir (poor person) becomes the owner of the goods or money, he can then spend the money in these causes if he wishes [Fatawa-e-Alamghiri].”

Allah knows the best.