At 8 a.m., the body was discovered in a pool of blood by a security guard. The incident occurred in Mahipat Mau village of Kakori, on the city outskirts.
The deceased was identified as Imtiaz, from Kushinagar.
According to the police, he had a verbal spat with his son-in-law, Salamat, late on Tuesday when he had come to visit him.
Imtiaz, who had been living in the mosque for the past three years, has been an attendant there and would run small errands like cleaning up and collecting water, an official told IANS.
Neighbours told the police that as he was regular with his morning prayers, his absence on Wednesday was immediately noticed.
Superintendent of Police (rural) Gaurav Grover said that their prime suspect was the son-in-law. The police was trying to locate Salamat. The body has been sent for autopsy.