Villegas went into education after his retirement, and in 1876 he founded the school La Paz. He published several reports and educational textbooks in the 1880s, and in 1889 President Juan Pablo Rojas Paul named him Minister of Public Instruction. In 1892 Villegas was appointed the president of the Federal Council. Villegas served as interim President of Venezuela for the final time in 1892, when Raimundo Andueza Palacio was in absentia while dealing with the outbreak of the Legalist Revolution. Villegas resigned later that year and was succeeded by his nephew Guillermo Tell Villegas Pulido. Returning to education, he published the first Venezuelan popular instruction book on literature, science, and fine arts in 1895. In 1901, he was elected as a member of the at the age of 80.