We present a theory of the non-linearities of the spin Seebeck effect (SSE) in a ferromagnetic nanowire at cryogenic temperatures. We adopt a microscopic quantum noise model based on a collection of two-level systems. At certain positions of Pt detectors to the wire, the transverse SSE changes sign as a function of temperature and/or temperature gradient. On the other hand, the longitudinal SSE does not show significant non-linearities even far outside the regime of validity of linear response theory.