He was the founder and administrator of several Swiss colonies, most prominently Nueva Helvecia in Uruguay and San Bernardino in Paraguay.

In 1855, he married Katharina Karoline Müller (1828-1861) originally from Unterambringen (Kingdom of Württemberg) and the couple had two sons; Jakob Emil Anton (1856-1929) and Hans Otto (1857-1935).

Then he travelled through Argentina, Carmen de Patagones and Santa Fe, and settled in 1869 in Paraguay, in the area of Caazapá, where he married Elizabeth Vera and had two other sons: Santiago Guillermo and Eduardo Schaerer.

Years later his other sons, Emil Jakob and Hans Otto, came from Switzerland and also settled in Paraguay.

Santiago Schaerer died in Asuncion, Paraguay, on January 28, 1895, at 60 years of age.