At that time Giri Kedaton had high popularity among Islamic intellectuals, so that many students from all over the archipelago came to study religion.
H. J. de Graaf and Samuel Wiselius also called the Giri pesantren the "kingdom of ulama" (Geestelijke Heeren).
Almost all important events related to changes in leadership at the center of the Islamic kingdom at that time had to be carried out in Giri Kedaton, not only a religious school but also a unity that had political power.
In that meeting, the regents of East Java agreed to recognize Pajang's power as a continuation of the Demak Sultanate.
Sunan Prapen was also the pacifier of the war between Panembahan Senopati the king of Mataram against Jayalengkara, the regent of Surabaya in 1588.
The war was motivated by the refusal of the regents of East Java to the power of Senopati which had brought down the Sultanate of Pajang.
Sultan Agung also appointed his brother-in-law, Prince Pekik, the son of Jayalengkara from Surabaya, to face Giri.
Sunan Kawis Guwa was invited to continue to lead Giri on the condition that he submit to Mataram.