Former Prime Minister Mohamed Abdullahi Farmajo succeeded Hassan Sheikh Mohamud to become the east African country's next president, during a service at Mogadishu airport on Wednesday.
World Watch Monitor, a Christian organisation which reports on Christian under pressure for their faith, said: "Although closely watched by international observers, little is expected to change for the small community of Somali Christians after these elections."
Somalia has recently been gripped by an ongoing Islamic insurgency involving al-Shabaab, a corruption crisis and the threat of famine.
Before his inauguration in 2012, former president Mohamud said he was dedicated to forming a Somalia "at peace with itself and with its neighbours, a Somalia that values kindness, respect and human rights".
This year, however, Somalia, rose from seventh to second in the World Watch List rankings by Open Doors which highlights countries where persecution against believers.
WWM claims jihadists and tribal leaders are targeting Christians in rural areas "with impunity", while believers who have converted from a Muslim background all over the nations are being unfairly treated by "communities and authorities".
The organisation said: "Even as a new president takes charge, the country's constitution leaves little room for changes in the realm of freedom of religion or belief."
Article 17 of Somalia's constitution implies every person is free to practice their religion, however, no religion other than Islam can be promoted publicly.
Article 2 indicates that no legislation which does not adhere to the general principles of Sharia - Muslim religious law - may be enacted in the country.