The objective of this study was to compare the effect of freeze-dried acid whey on physicochemical properties and microbial changes of organic fermented sausages made from beef and fallow deer meat. Five formulations of sausages from each species were made. The results show that processing time and species of meat were the high significant factor on tested parameters. Variants and interactions between main factors influenced at different levels of significance on some tested attributes. At the end of processing fallow deer sausages were characterised by the lower pH (4.79 ± 0.01–4.90 ± 0.02 for fallow deer and 5.04 ± 0.00–5.25 ± 0.03 for beef sausages) and the content of 2-thiobarbituric acid reactive substances (1.54 ± 0.09–2.81 ± 0.23 and 1.64 ± 0.15–5.06 ± 0.25 respectively) than sausages made from beef meat. In conclusion, the addition of freeze-dried acid whey in varying amounts did not significantly affect the physicochemical characteristics of sausages from both fallow deer and beef. However, further research is needed to compare the effect of acid whey on the nutritional values of raw fermented sausages from fallow deer and beef.