Jinnah ya kasance daga Gujarati Ismaili baya, ko da yake Jinnah daga baya ya bi koyarwar Twelver Shi'a. Bayan mutuwarsa, danginsa da sauran shaidu sun yi iƙirarin cewa ya tuba daga baya a rayuwa zuwa darikar Sunni. Addininsa a lokacin mutuwarsa an yi jayayya a shari'ar kotu. Jinnah ya fito ne daga wani attajirin attajiri, mahaifinsa attajiri ne kuma an haife shi ne a cikin dangin kiristocin da ke zaune a ƙauyen Fatli a cikin gundumar Fatli a cikin gundumar Gondar, yanzu a Sindh, Pakistan amma a cikin Bombay Shugabancin Biritaniya Indiya.
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