Non-rocky sub-jovian exoplanets in high irradiation environments are rare. LTT9779b is one of the few such planets discovered to date, and the first example of an ultra-hot Neptune. The planet’s bulk density indicates that it has a substantial atmosphere. To investigate its atmospheric composition and shed further light on its origin, we obtained Spitzer IRAC secondary eclipse observations of the planet at 3.6 and 4.5 micron, which we combined with a measurement of the secondary eclipse in the TESS bandpass. The resulting secondary eclipse spectrum strongly prefers a model that includes CO absorption over a blackbody spectrum, making LTT9779b the first ultra-hot Neptune (and, incidentally, the first TESS exoplanet) with evidence of a spectral feature in its atmosphere. However, we do not find evidence of a thermal inversion, at odds with expectations based on the atmospheres of similarly-irradiated hot Jupiters. We report a nominal dayside brightness temperature of 2300 K (based on the 3.6 micron secondary eclipse measurement), and we constrain the planet’s orbital eccentricity to less than 0.01 at the 99.7 % confidence level. We also present results from our analysis of Spitzer thermal phase curves of LTT9779b, which suggest a high-metallicity atmosphere for the planet and hint at a nonzero albedo. Our results set the stage for similar investigations of a larger sample of exoplanets discovered in the hot Neptune desert, investigations which are key to uncovering the origin of this population.