Olive oil pomace (OOP) is a bio-waste rich in highly soluble polyphenols. OOP has been proposed as an additive in ruminant feeding to modulate rumen fermentations. Three groups of ewes were fed the following different diets: a control diet and two diets supplemented with OOP, obtained with a two-phase (OOP2) or three-phase (OOP3) olive milling process. Rumen liquor (RL) showed a higher content of 18:3 cis9 cis12 cis15 (α-linolenic acid, α-LNA) with OOP2 inclusion, and of 18:2 cis9 trans11 (rumenic acid, RA) with OOP3 inclusion. The overall composition of the RL microbiota did not differ among treatments. Significant differences, between control and treated groups, were found for six bacterial taxa. In particular, RL microbiota from animals fed OOPs showed a reduction in Anaerovibrio, a lipase-producing bacterium. The decrease in the Anaerovibrio genus may lead to a reduction in lipolysis, thus lowering the amount of polyunsaturated fatty acids available for biohydrogenation. Milk from animals fed OOP showed a higher content of 18:1 cis9 (oleic acid, OA) but the α-LNA concentration was increased in milk from animals treated with OOP2 only. Therefore, inclusion of OOP in ruminant diets may be a tool to ameliorate the nutritional characteristics of milk.