Agro-industrial by-products might substitute conventional feedstuff in animal nutrition, in order to decrease the cost of their disposal, limit the environmental impact of feed production, and reduce feed-food competition. Nut industries generate a huge amount of fibrous by-products that are also a source of bioactive compounds, such as tannins, and have a notable lipid content, largely composed by unsaturated fatty acids (FA). Therefore, this study was conducted to examine the effects of partial replacement of maize with almond, hazelnut, and pistachio kernel skins at three doses [70, 140, and 210 g/kg dry matter (DM)] on ruminal fermentation and biohydrogenation. The study was performed in vitro with batch cultures of rumen microorganisms, using cannulated ewes as donors of rumen inocula. Total gas and methane production, ammonia, and volatile fatty acid concentration, and dry matter disappearance were analysed as indicators of rumen fermentation. To study ruminal biohydrogenation, in vitro digesta fatty acid profile was examined by gas chromatography. Pistachio skins did not affect any ruminal fermentation parameter. On the contrary, the highest doses of almond and hazelnut skins were capable of reducing gas and methane production and ammonia concentration. However, the highest levels of almond and hazelnut skins, as well as the medium dose of the latter, also reduced the production of volatile fatty acids. Most of these effects were probably due to the presence of tannins. Concerning in vitro ruminal biohydrogenation, FA profile showed that the inclusion of nut skins in the diet favored the accumulation of potentially health-promoting poly- and mono-unsaturated FA (e.g., trans-11 18:1), without a trans-10 shift. On the other hand, medium and high levels of almond and pistachio caused an increase in undesirable FA, such as trans-10 18:1 and trans-10 cis-12 18:2. Effects on biohydrogenation are mainly attributed to the phenolic compounds in nut skins. Further research would be advisable to verify if these findings are maintained under in vivo conditions.