The Nigerian state being a hybrid and heterogeneous society reflected a peculiar legal system comprised of the received English laws as well as the Statutes of general application that was in force as at 1900, and furthermore, the customary and native laws operational within the southern part of Nigeria, and the Islamic law of the Maliki school applicable in the predominant Moslem North of the country. Consequent on the above, the legal history of the country Nigeria accommodated both the criminal and the penal codes serving both the Northern and Southern divides and reflected mostly the socio-cultural regimes common with regions. Having this as a background, the practice of plea bargain was introduced vide the provision of the Economic and Financial crimes commission. The authors therefore strived to reconcile the practice of plea bargain (introduced in 2004) in a secular and multicultural society, notwithstanding the fact that the customary and sharia laws of the various ethnic groups in Nigeria operating in the Northern and Southern regions is devoid of the concept of plea bargain. Significantly, the introduction and practice of plea bargain portends a challenge in operation against the traditional criminal justice system. The paper therefore maintained that the introduction and practice of plea bargain though a positive step, is however laden with challenges both in administration and operation.