On a human level, Bediuzzaman saw religion as representing the heart and conscience, and science, the reason; both were necessary for true progress to be attained. He explained it as follows: "The religious sciences are the light of the conscience, and the modern sciences are the light of the reason. The truth becomes manifest through the combining of the two. The studcnts' endcavour will take flight on these two wings. When they are separated it gives rise to bigotry in the one, and wiles and scepticism in the other."

On a wider scale, the Medresetu'z-Zehra would unite the three traditions in the educational system by representing "the most superior mekteb by the " reason, the very best medrese by the heart, and the most sacred zawiye by the conscience." As a result of its unique value for the Islamic world, it ; would in time gain financial independence by reason of the donations and pious bequests it would receive.

The benefits of such a system would be manifold. Just as it would ensure the future of the ulema in the eastern provinces, at the same time it would be step towards the unification and reform of general system. So would it deliver Islam from the bigotry, superstitions, and false beliefs which had encrusted parts of it over the centuries. And, importantly, would be a means of introducing modern learning into the medreses in a way which would allay the ulema’s suspicions concerning modern science. Also, it would "open the door to spreading the beneficial aspects of constitutionalism."

Bediuzzaman wished for Islam to function like a consultative council, that is to say, through the mutual consultation (sura) of "the three divisions of the army of Islamic education", those of the medreses, the mektebs, and the tekkes, so that "each would complete the deficiencies of the other". His aim was for the Medresetu'z-Zehra to be an embodiment of this.

According to Bediuzzaman, this transforming the medreses