The first major defeat for Raghudev was at the hands of Isa Khan, an Afghan chief from Mymensingh. Raghudev fortified Jangalbari in Mymensingh, but ultimately lost the region south of Rangamati sometime before 1594. After Man Singh became the Subahdar of the Mughal Empire for Bengal in 1594, Isa Khan and others were defeated by the Mughals under Himmat Singh in 1596, forcing Isa Khan to ally with Raghudev. Raghudev, with the help of Isa Khan, attacked Koch Bihar, and Lakshmi Narayan submitted on his own accord to vassalage of the Mughal Empire. Under these circumstances, Raghudev transferred his capital from Barnagar to north Guwahati.