On the basis of the isomer-specific effects of trans fatty acids (FA) on human health, and the detrimental effect of t10,c12-conjugated linoleic acid (CLA) on cows’ milk fat production, there is a need to identify factors that affect the shift from trans-11 to trans-10 pathway during ruminal biohydrogenation of FA. This experiment was conducted in vitro and aimed at separating the effects of the diet of the donor cows from those of the fermentative substrate, which is necessary to prevent this shift. A total of four dry Holstein dairy cows were used in a 4 × 4 Latin square design. They received 12 kg of dry matter per day of four diets based on maize silage during four successive periods: the control diet (22% starch, <3% fat); the high-starch diet, supplemented with wheat plus barley (35% starch, <3% crude fat); the sunflower oil diet, supplemented with 5% of sunflower oil (20% starch, 7.6% crude fat); and the high-starch plus oil diet (33% starch, 7.3% crude fat). Ruminal fluid of each donor cow was incubated for 5 h with four substrates having similar chemical composition to the diets, replacing sunflower oil by pure linoleic acid (LA). The efficiency of isomerisation of LA to CLA was the highest when rumen fluids from cows receiving dietary oil were incubated with added LA. The shift from trans-11 to trans-10 isomers was induced in vitro by high-starch diets and the addition of LA. Oil supplementation to the diet of the donor cows increased this shift. Conversely, the trans-10 isomer balance was always low when no LA was added to incubation cultures. These results showed that a large accumulation of trans-10 FA was only observed with an adapted microflora, as well as an addition of non-esterified LA to the incubation substrate.