This study entitled the effective learning process in shaping intellectual intelligence and learning motivation in students at Ma’had Ali Bin Abi Thalib Yogyakarta. The purpose of this study is to explain how the student’s effective learning process, knowing students’ intellectual intelligence and understanding students’ motivation. In addition, the purpose is to investigate whether there is any influence between the effective learning process with intellectual intelligence and learning motivation on students at Ma’had Ali bin Abi Thalib Yogyakarta. The type and approach of this research is field research with a qualitative (descriptive) approach. The research subjects were six (6) students. Data collection was done by the methods of interview, observation, and documentation. Data analysis techniques were done using reduction, presentation, withdrawal, and data credibility. The results of this study indicate that: 1) the effective learning process of students is that, in their learning activities, the aspect of attendance and work on assignments is categorized to be good. It is seen from the discussions, asking friends to repeat the material, and studying together. The place and learning organizations use The Genealogy of Lughah al-Arabiyah curriculum. The teachers also have motivated to learn and assist in understanding the material. Then the supporting factor comes from themselves because of their interest in learning Arabic. 2) Students’ intellectual intelligence is obtained by repeating the subject matter, listening to the teacher’s explanation, and asking friends and teachers. 3) Students’ learning motivation is the encouragement in learning Arabic and Islamic studies, the ability to speak active or passive Arabic, and the fact that Arabic is the science of learning the Qur’an. 4) Then the effect of the effective learning process can be seen from the students themselves, whether they were graduated from the Islamic boarding house or have studied Arabic before. It is because the obstacle that is often in students is the basic mastery of Arabic.