After the Battle of Sekigahara, he was given the 180,000 koku crop yield territory of Sawayama Omi Province (Hikone City, Shiga Prefecture), a former territory of Mitsunari ISHIDA, for services including making peace with Terumoto MORI, supreme commander of the Western Camp, supporting Kazutoyo YAMAUCHI in entering Tosa Province, mediating peace negotiations between the Tokugawa clan and the Shimazu clan to heal the wounds of war (Naomasa died before the peace negotiations were completed and Masanobu HONDA took over his task), and for his efforts in laying the groundwork for the Edo Shogunate.
関ヶ原の戦いの後は西軍の総大将を務めた毛利輝元との講和、山内一豊の土佐入国の援助、徳川氏と島津氏の和平交渉の仲立ち（直政自身は和平交渉が完全に終了する前に亡くなったので、その後の和平交渉の仲立ちの役目は本多正信に引き継がれた）などと言った戦後処理と江戸幕府の基礎固めに尽力し、これらの功によって、石田三成の旧領である近江国佐和山（滋賀県彦根市）18万石を与えられた。