Current flaxseed processing methods have shown limited or varying success in improving the fatty acid profile of milk beyond what is achieved with feeding unprocessed flaxseed. In this study, a novel method to “rumen-protect” flaxseed is proposed, which encapsulates flaxseed with soybean protein using a proprietary method (12BT40; N3Feed LLC; Tualatin, OR; 23.8% CF, 31.7% CP). To determine the long-term efficacy, 12 Jersey cows (blocked by parity) in mid lactation were fed 2.5 kg of 12BT40 for 8 weeks as top dressing to their TMR (2.9% CF, 14.8% CP). Milk and serum samples were collected at the end of wk 0, 2, 4, 6, and 8 and analyzed for fatty acid profile and metabolic indicators. Data were analyzed using PROC MIXED in SAS version 9.4. Fixed effects were supplementation (control, bypass flaxseed), week of supplementation (2, 4, 6, and 8), their interaction, and parity (primiparous, multiparous) and baseline concentration as linear covariate; a first-order heterogeneous autoregressive variance-covariance structure was fitted for repeated measures within cows. Bypass flaxseed supplementation consistently increased throughout the supplementation period milk production (+4.42 ± 1.52 kg/d; P = 0.02) without significant changes in milk composition. In regards to milk fatty acid profile, bypass flaxseed supplementation consistently increased C18:3n-3 proportions throughout the supplementation period (+1.91 ± 0.20 wt% FA; P < 0.0001). In conclusion, feeding rumen-bypass flaxseed is a potential management tool to improve the nutritional value of milk and dairy products, while at the same time increasing milk yield.