Stevens was a controversial governor in his time, and has become more controversial in retrospect. He used a careful combination of intimidation and force to compel the Native American tribes of Washington Territory to sign treaties that handed over most of their lands and rights to Stevens' government. These included the Treaty of Medicine Creek, Treaty of Hellgate, Treaty of Neah Bay, Treaty of Point Elliott, Point No Point Treaty, and Quinault Treaty. When Stevens was met with resistance, he used the troops at his disposal to exact vengeance. His winter campaign against the Yakama tribe, led by Chief Kamiakin, and his execution of the Nisqually chieftain Leschi (for the crime of having killed Stevens' soldiers in open combat), among other deeds, led a number of powerful citizens in the territory to beg Pierce to remove Stevens. Territorial Judge Edward Lander and Ezra Meeker (an influential private citizen) were both vocal in opposing Stevens—Lander was arrested as a result, and Meeker was simply ignored. Pierce sent word to Stevens of his disapproval of Stevens' conduct, but refused to remove the governor. Those who opposed Stevens ultimately lost public support, as the majority of the citizens of Washington Territory saw Meeker as being on the side of the "Indians", and Stevens on the side of the white settlers.

As a result of this public perception, Stevens was popular enough to be elected the territory's delegate to the United States Congress in 1857 and 1858. The tensions between the whites and the Native Americans would be left for others to resolve—Stevens is often charged with responsibility for the later conflicts in eastern Washington and Idaho, especially the war fought by the United States against Chief Joseph and the Nez Perce, but these events were decades away when Isaac Stevens left Washington for good in 1857.