At the turn of the 20th century, the Muslim community in the Malabar area of Kerala was in a state of decline. Ignorance, superstitions, and moral degradation had permeated the society. Educational institutions were impoverished and neglected, and religious practices had become ritualistic and detached from practical life. The isolation of religion from the contemporary world left religious scholars disconnected and ill-equipped to address the challenges posed by modern thoughts and sciences. Islam faced attacks from various fronts, further exacerbating the critical situation. Amidst these circumstances, a group of sincere and visionary scholars emerged. They held steadfast to the pure doctrines of Islam and were influenced by the teachings of scholars. One prominent leader among this group was Thayyil Mohammed Moulavi, a renowned theologian and spiritual guide. These scholars recognized the urgent need for reformation and revitalization within the Muslim community. They understood the importance of integrating religious teachings with practical life and engaging with contemporary issues. With their wisdom and enlightened vision, they sought to address the decadence and divisions prevailing among the Muslims of Malabar.

Kerala Nadwathul Mujahideen was formed by esteemed scholars who were dedicated to promoting true faith and knowledge among the Muslim community. Their discussions and correspondence with other Muslim scholars led to the establishment of this ideological, cultural, and educational reform association. The primary objective of Kerala Nadwathul Mujahideen was to foster harmony and cooperation within the Muslim society by purifying their faith from superstitious beliefs and promoting moral and educational reforms. The association was officially registered under the society act XXI of 1860 with registration number 2/57. Its inaugural session took place in Calicut city in 1950, with Thayyil Mohammed Moulavi presiding over the meeting. During this session, the importance of resolving differences within the Muslim society, fostering unity and cooperation, and updating the outdated syllabi of Arabic Madrasas were emphasized. Kerala Nadwathul Mujahideen laid the foundation for various educational, cultural, and social initiatives, including the establishment of Jamia Nadwiyya. The organization has played a significant role in promoting religious understanding, educational reforms, and the overall progress of the Muslim community in Kerala.

Jamia Nadwiyya was established in 1964 as an Islamic University, with a vision to address the educational, cultural, and economic challenges faced by the Muslim community in the aftermath of the Malabar revolt of 1921. The founders, belonging to Kerala Nadwathul Mujahideen, recognized the need for practical measures to uplift their community and prevent its decline. They sought to blend Islamic culture with the knowledge and advancements of the Western world.With its establishment in Edavanna, Malappuram district, Jamia Nadwiyya quickly gained recognition as a modern institution for Muslim theological learning and Arabic studies. It focuses on imparting knowledge in Quranic sciences, the traditions of Prophet Muhammad (peace be upon him), Arabic language, literature, and modern sciences. The establishment of Jamia Nadwiyya was based on a resolution passed by the state council of Kerala Nadwathul Mujahideen. Since its inception, the institution has been committed to providing quality education in a harmonious blend of Islamic and modern knowledge, aiming to empower the Muslim community and contribute to their progress.