Sheik Mutumba said he thought he had married a woman in their traditional Islamic ceremony in December.
He claimed he hadn't been intimate with his "wife" since the wedding because she told him she was menstruating.
After the arrest, the bride revealed to police his real name was Richard Tumushabe, according to local reports.
He posed as a woman so he could marry the imam and allegedly planned to steal his money.
The move to suspend the groom from his duties at Kyampisi Masjid Noor mosque was intended to preserve the integrity of their faith, according to Sheik Isa Busuulwa, the head imam of Masjid Noor of Kyampisi.
The Daily Monitorsaid an investigation was pending over the "unfortunate incident".
"He has been one of the three imams of the mosque. He had spent about four years preaching in this mosque on top of teaching Islam to children," Sheik Busuulwa told the Ugandan independent daily newspaper.
The bilal at the mosque where Mutumba has been relieved of his duties had seen "Swabullah" attending prayers.
"He had a sweet soft voice and walked like a woman. She also always dressed in either gomesi or hijab," Amisi Kibunga told the Daily Monitor.
"Four days after their wedding, the groom came to me complaining that his 'bride' had refused to undress while they slept. Actually, I was planning to go to their home to counsel 'her' when I heard she had been arrested in connection with theft of a television set and clothes of their neighbour," Mr Kibunga added.
Local sources revealed Sheik Mutumba was devastated by the incident and needed counselling.