[1][2] His brother John Eliot Thayer I had been operating a successful banking firm in Boston.

[citation needed] He was known as the “honest banker” because he sold money at the legal rate unlike most, for the time.

In 1865 Nathaniel Thayer II retired, sold his business to his partners and lived primarily in The Homestead for “he preferred the woods and fields to the streets and crowds”.

He contributed to a commons hall, erected Thayer Hall in 1870 as a memorial of his father and brother, bore the expenses of Louis Agassiz's 1865-66 expedition to South America (known as the Thayer Expedition; which his son Stephen Van Rensselaer Thayer also joined as a research assistant), built a fire-proof herbarium at the botanic garden, and gave much in aid of poor students of the college.

Together, they had seven children:[4] Although Nathaniel Thayer II lived in Boston for many years, he always regarded himself as belonging to Lancaster.