Officials said Sheikh Muhammad Abas Kirevu had recruited for cells run by the Allied Democratic Forces (ADF) - rebels who have pledged allegiance to the Islamic State group.
He was killed just outside Kampala.
At least four people were killed by attackers on motorbikes who blew themselves up in the city on Tuesday.
More than 30 others were injured in the attack, which IS said it was behind and officials have blamed on the ADF.