During his term Runnels consistently supported Southern positions. He frequently asserted that Texas might be forced to secede from the Union, supported the unsuccessful effort to put the Texas legislature on record in favor of reopening the African slave trade, and signed into law a bill allowing free blacks to choose a master and become slaves. He also signed into law the bill that appropriated financial support to establish the University of Texas and the bill establishing the State Geological Survey. The most vexing problem Runnels faced during his term as governor was the problem of protecting frontier settlers against Indian depredations. The year he took office there was a marked upsurge in Indian attacks, generally by the Comanches. Although Runnels supported and signed into law bills that called for the raising of temporary ranger battalions to meet the emergency, he opposed efforts to form permanent battalions on the grounds that the state could not afford them and that the federal government was responsible for protecting the frontier. When angry settlers took matters in their own hands and retaliated against Indians on the Brazos Indian Reservation, they clashed with the army. Runnels's efforts to make peace failed. In 1859 the state Democratic convention renominated Runnels, and Houston again declared himself a candidate. This time however, Houston's key issues were his record of service to the state, particularly at the battle of San Jacinto, and Runnels's record as governor. Houston made particularly effective use of the problems on the frontier and the African slave-trade issue. The Democratic party attempted to blunt the criticism on the slave-trade matter by remaining silent on the controversy in their platform, but they were largely unsuccessful. The combination of Runnels's mediocre record as governor and Houston's personal popularity resulted in a reversal of the 1857 results, and Houston defeated Runnels by a vote of 36,227 to 27,500.
Runnels subsequently retired to his plantation in Bowie County but remained active in the Democratic party. He was a member of the Secession Convention in 1861, where he was a vigorous supporter of the secession resolution. After the Civil War, although he had not yet received a pardon from the president, he was a delegate to the Constitutional Convention of 1866. At this convention he was one of about eleven delegates who were often termed the "aggressive secessionists" or the "irreconcilables." Although this group nominated him for convention president, he was not elected, and his extreme reluctance to seek or endorse workable compromises negated any influence he might have had on the convention's deliberations. In the 1850s Runnels built an impressive Greek Revival mansion near Old Boston and furnished it in anticipation of his approaching marriage. For some reason the wedding never took place, and he remained a bachelor for the rest of his life. When the Texas Historical Society was organized in Houston on May 23, 1870, Runnels was elected one of its vice presidents. He was also a member of St. John's Masonic Lodge. He died on December 25, 1873, and was buried in the Runnels family cemetery in Bowie County. In 1929 his remains were exhumed and reinterred in the State Cemetery at Austin, where a monument was installed at his new grave.
30° 15.933, -097° 43.639
Texas State Cemetery