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Simple Summary: Cows emit the greenhouse gas methane (CH4) as a result of microbial feed digestion. Methane emissions can be reduced by adopting nutritional strategies, such as dietary supplementation of linseed. Additionally, the oil in linseed increases the proportion of favorable fatty acids in milk fat. This study evaluated the effect of linseed on CH4 emission and milk fatty acid composition measured in a group of cows in a naturally ventilated barn and in individual cows in respiration chambers. The substantially higher proportions of favorable fatty acids in the milk of linseed-fed cows were detected in individual milk samples and in the milk of the herd. Therefore, the analysis of bulk milk could be a suitable control instrument for retailers. Visualizing the course of CH4 emissions over a whole day showed slightly lower CH4 values in linseed-supplemented individuals and groups. However, we found no significant reduction of CH4 as a result of linseed supplementation. Feed supplements in concentrations that are effective in reducing CH4 must show whether the reduction potential is comparable when determined at the group and individual levels. The present study evaluated the effects of linseed supplementation on CH4 emission and milk fatty acid composition in dairy cows measured at the group level in an experimental dairy loose housing using a tracer gas technique and individually in tied stalls and respiration chambers. Cows (2 × 20) were maintained in two separate sections under loose-housing conditions and received a diet supplemented with extruded linseed (L) lipids (29 g·kg−1 dry matter) or a control (C) diet containing corn flour. Subsequently, 2 × 6 cows per dietary group were investigated in a tied-housing system and respiration chambers. Substantially higher proportions of favorable milk fatty acids were recovered in L cows when compared with C cows at the group level, making the analysis of bulk milk a suitable control instrument for retailers. Linseed supplementation resulted in a slightly lower diurnal course of CH4 emission intensity than the control at the group and individual levels. However, we found no more than a trend for a CH4 mitigating effect, unlike in other studies supplementing similar linseed lipid levels. Feed supplements in concentrations that lead to a significant reduction in CH4 emissions must show whether the reduction potential determined at the group and individual levels is comparable. [ABSTRACT FROM AUTHOR]