The present study examined the effect of the type of meat (beef and fallow deer) and the addition of freeze-dried acid whey on nutritional values and the content of bioactive compounds (peptides, L-carnitine, glutathione, and conjugated linoleic acid (CLA)) in uncured fermented sausages. The antioxidant properties of isolated peptides (ABTS, DPPH radical scavenging activity, and ferric-reducing antioxidant power) were also evaluated. The results showed that fallow deer sausages had higher peptide content than beef products. The addition of acid whey caused a decrease in the content of peptides, especially in fallow deer sausages. The glutathione content in beef sausages (22.91–25.28 mg 100 g−1 of sausage) was quite higher than that of fallow deer sausages (10.04–11.59 mg 100 g−1 of sausage). The obtained results showed a significantly higher content of CLA in beef sausages than in products from fallow deer meat. In conclusion, products prepared from fallow deer meat have generally higher nutritional value because of the content of peptides, their antioxidant properties, and the content of L-carnitine, while beef products have higher levels of CLA and glutathione.