Direct comparison of cow and goat performance and milk fatty acid responses to diets known to induce milk fat depression (MFD) in the bovine reveals relevant species-by-diet interactions in ruminal lipid metabolism. Thus, this study was conducted to infer potential mechanisms responsible for differences in the rumen microbial biohydrogenation (BH) due to diet and ruminant species. To meet this objective, 12 cows and 15 goats were fed a basal diet (control), a similar diet supplemented with 2.2% fish oil (FO), or a diet containing 5.3% sunflower oil and additional starch (+38%; SOS) according to a 3 × 3 Latin square design with 25-d experimental periods. On the last day of each period, fatty acid composition (by gas chromatography) and bacterial community (by terminal-RFLP), as well as fermentation characteristics, were measured in rumen fluid samples. Results showed significant differences in the response of cows and goats to dietary treatments, although variations in some fermentation parameters (e.g., decreases in the acetate-to-propionate ratio due to FO or SOS) were similar in both species. Main alterations in ruminal BH pathways potentially responsible for MFD on the SOS diet (i.e., the shift from trans-11 to trans-10 18:1 and related increases in trans-10,cis-12 18:2) tended to be more pronounced in cows, which is consistent with an associated MFD only in this species. However, changes linked to FO-induced MFD (e.g., decreases in 18:0 and increases in total trans-18:1) were stronger in caprine rumen fluid, which may explain their unexpected susceptibility (although less marked than in bovine) to the negative effect of FO on milk fat content. Altogether, these results suggest that distinct ruminal mechanisms lead to each type of diet-induced MFD and confirm a pronounced interaction with species. With regard to microbiota, differences between cows and goats in the composition of the rumen bacterial community might be behind the disparity in the microorganisms affected by the experimental diets (e.g., Ruminococcaceae, Lachnospiraceae, and Succinivibrionaceae in the bovine, and Pseudobutryrivibrio, Clostridium cluster IV, Prevotella, and Veillonellaceae in the caprine), which hindered the assignation of bacterial populations to particular BH steps or pathways. Furthermore, most relevant variations in microbial groups corresponded to as yet uncultured bacteria and suggest that these microorganisms may play a predominant role in the ruminal lipid metabolism in both cows and goats.