The production of oxygenated bio-additives for traditional fuels represents a key challenge due to their depletion in the near-future and their positive contribution to the reduction in environmental pollution. The present study considers the synthesis of 1-hexanol/hexyl hexanoate mixtures, two oxygenated Diesel bio-additives produced through the hydrogenation of hexanoic acid, obtainable from the fermentation of a wide variety of waste biomasses. In our case, crude hexanoic acid was produced through the fermentation of grape pomace, an abundant Italian agrifood waste. Commercial 5 wt% Re/γ-Al2O3 was adopted for the catalytic hydrogenation of crude hexanoic acid, and the support acidity allowed the tuning of the reaction selectivity toward the formation of hexyl hexanoate, instead of 1-hexanol, reaching yields of 40 and 25 mol%, respectively. The effects of each bio-additive on Diesel engine performance and exhaust emissions (soot, nitrogen oxides, carbon monoxide, unburned hydrocarbons) were evaluated, highlighting noteworthy positive effects especially on the reduction in carbon monoxide and soot emissions, if compared with those of Diesel fuel alone. Similar promising performances were achieved by employing Diesel blend mixtures of 1-hexanol/hexyl hexanoate, mimicking typical compositions of the rhenium-catalyzed post-hydrogenation mixtures. Even in such cases, 1-hexanol/hexyl hexanoate mixtures can be blended with commercial Diesel fuel, up to high loadings currently not yet investigated (20 vol%), without altering the engine performances and, again, significantly lowering soot and carbon monoxide emissions by more than 40%. This work highlights the possibility of obtaining such oxygenated bio-additives starting from waste through to a fully sustainable process and proves their beneficial effects on the reduction in exhaust emissions with no changes in engine performance.