In 1996, he obtained a master's degree in Public administration from the Gadjah Mada University.

In 2008, Effendy successfully completed his Doctoral program in military sociology from the Airlangga University.

In addition, Muhadjir has also published several books such as "Bala Dewa", "As Witnessed Dahlan Young", "Masyarakat equilibrium: meniti perubahan dalam bingkai keseimbangan",[6] "Pedagogi kemanusiaan: sebuah refleksi multidimensional" as well as "Muhammadiyah and Education in Indonesia".

Muhadjir becomes centre of controversy when he made a statement of a webinar that "the rich should marry the poor" and urged the Minister of Religious Affairs to declare a fatwa about it.

His proposal later caused backlash among internet users and accused him of hurting the feelings of the poor citizens.