Naeff studied law in Heidelberg (Germany), and, after his return to Switzerland, he was elected to the cantonal (state) government of St. Gallen.
Naeff is well known for not intervening in the conflict, which dominated Switzerland at that time, between liberals and conservatives.
The Rhine Valley was a stronghold of the liberals, which is why Naeff could depend on his supporters.
He was elected to the Swiss Federal Council of ministers on 16 November 1848, as a representative of St. Gallen.
While, in his long term in office, Naeff increasingly lost influence and adhered a reputation as "deadhead".