Flaxseed (FS) and chia seed (CS) are oilseeds rich in omega-3 fatty acids, which may change meat and milk composition when added to ruminants' diets and may have health benefits for humans. Literature on the effects of CS supplementation on ruminal metabolism is nonexistent. A dual-flow continuous culture fermenter system consisting of 6 fermenters was used to assess the effect of FS and CS supplementation in an alfalfa hay-based diet on ruminal fermentation, nutrient digestibility, microbial protein synthesis, and long-chain fatty acid flow. Diets were randomly assigned to fermenters in a replicated 3 × 3 Latin square design, with 3 consecutive periods of 10 d each, consisting of 7 d for diet adaptation and 3 d for sample collection. Each fermenter was fed a total of 72 g of DM/d divided in 6 equal portions. Treatments were 1) alfalfa hay + calcium soaps of palm oil fatty acid (MEG; 69.3 g DM/d of alfalfa hay plus 2.7 g DM/d of calcium soaps of palm oil fatty acid), 2) alfalfa hay + FS (FLAX; 68.4 g DM/d of alfalfa hay plus 3.6 g DM/d of ground FS), and 3) alfalfa hay + CS (CHIA; 68.04 g DM/d of alfalfa hay plus 3.96 g DM/d of ground CS). Dietary treatments had similar amounts of total fat, and fat supplements were ground to 2-mm diameter. Effluents from the last 3 d of incubation were composited for analyses. Data were analyzed using the MIXED procedure of SAS. Ruminal apparent and true nutrient digestibility of all nutrients did not differ ( > 0.05) among treatments. Compared with MEG, FLAX and CHIA increased the flows of C18:3 -3, C20:4 -6, and total PUFA ( < 0.01). Both CHIA and FLAX treatments had greater ruminal concentrations of C18:0, indicating that both CS and FS fatty acids were extensively biohydrogenated in the rumen. The NH-N concentration, microbial N flow, and efficiency of microbial protein synthesis were not affected ( > 0.05) by treatments. Lastly, there were no differences ( > 0.05) among diets for total VFA concentration and molar proportions of individual VFA. Results from this study indicate that FS and CS supplementation did not impair ruminal fermentation, digestibility, microbial efficiency, and ruminal N metabolism. Overall, CS appears to be as effective as FS as a fat source when added to ruminants' diets using a dual-flow continuous culture system.