"A suicide bomber strapped with an IED exploded himself in Alhaji Haruna Mosque" in the Monday Market area, said Aderemi Opadokun, police commissioner of Borno state, of which Maiduguri is the capital.
Another bomb exploded Saturday afternoon near Maiduguri's main market, killing at least one person.
Meanwhile Earlier the city was attacked by Boko Haram terrorists, who fired a barage of rocket-propelled grenades that killed at least 13 people.
The dawn grenade attack was a new tactic in the extremist group's birthplace.
More than 1.5 million Nigerians have been forced from their homes by the nearly six-year-old terrorist attack in the northeast which has killed an estimated 13,000 people.
A multinational offensive this year forced the insurgents from towns where they had declared an “Islamic caliphate” but the extremists continue to carry out suicide bombings and hit-and-run attacks.