Yawancin mazauna birnin Maiduguri dai Musulmai ne. Amma akwai mabiya addini krista da dama a garin. Akwai manyan majami'o'i a garin kamar babban majami'an dake kan titin Kiri Kasamma. Maiduguri yayi suna kwarai wajen karatun alkur'ani a inda dalibai daka dukkan fadin Najeriya suke zuwa garin don neman ilmi. Manyan masallatai a garin sun hada da masallachin Mai Deribe, masallacin Madinatu, Masallacin Kofar Shehu, Masallacin Indimi da Masallacin Ibrahim Saleh. Akwai shahararrun malaman addinin Musulunci da dama a Maiduguri. A shekaran 2009, wani malamin addinin Muslunci wanda aka fi sani da Mohammed Yusuf ya tada fitina a garin a inda yake ikirarin ya'ki da gwamnati da kuma ilmin boko wanda a ganinsa yana lalata al'umma. Sanda aka yi wajen mako guda ana fafatawa tsakanin sojoji da 'yan sanda da kuma magoya bayan Mohammed Yusuf. Wannan tarzoma tayo sanadiyyar rasa rayuka da dama. Daga karshe jami'an gwamnati sun ci galba kan Mohammed Yusuf wanda sojoji suka cefke kuma suka dan'ka a hannun 'yan sanda. A hannun 'yan sandan Mohammed Yusuf ya rasu. 'Yan sanda sun yi ikirarin cewa ya rasu ne a yayin da ake bindige shi lokacin da yake kokarin kubucewa. Masu bin hakkin bil Adama sun yi harsashen cewa kisan gilla a kayi masa.