After his release he returned to the General Assembly, where he served until 1796. He was known as an active legislator and an advocate for the confiscation of Loyalist property. Like John Rutledge, Edward Rutledge opposed the Jay Treaty and the Anglophilic stance he perceived in the Federalist Party. As an elector in the 1796 Presidential Election, Rutledge voted for the two Southern candidates, Republican Thomas Jefferson and Federalist Thomas Pinckney. Rutledge had not been close with the eventual Victor John Adams dating back to their days in the Continental Congress, but he approved of Adams's defense policies towards France during the Quasi-War. The opposition afforded Adams's measures by Vice President Jefferson and the Congressional Republicans angered Rutledge because he now saw the Republicans as more partial to France than to American interests, a situation similar to the pro-British feelings he sensed in the Federalists during the Jay Treaty debates. Rutledge thereafter ceased communication with Jefferson. Rutledge served in the state senate for two years, then was elected governor in 1798.

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