In organic dairy farming supply with metabolizable protein (MP) is often limited. Therefore, the potential for increased MP concentration by increased pre-wilting of grass-clover before ensiling was investigated. Spring growth and first regrowth grown by 2 Danish organic farmers were cut and pre-wilted to a planned dry matter (DM) content of 35% and 70%, respectively, giving in total 8 silages with DM contents ranging from 28.3 to 72.5%. Four rumen, duodenal and ileal fistulated Holstein dairy cows (551 ± 33 kg body weight, 216 ± 23 d in milk, mean ± SD) were fed ad libitum with the silages in a crossover design, with 5 periods of 3 weeks. No concentrate was offered, but minerals and vitamins were offered daily. Three markers (Cr₂O₃, TiO₂ and YbCl₃·6H₂O) were dosed in the rumen twice a day for measurement of flow at duodenum and ileum. In the last week of each period daily feed intake was registered and 12 subsamples from duodenum and ileum, respectively, were collected over 94 h to cover the diurnal variation, pooled, and subsequently analyzed. Microbes were isolated from the rumen and analyzed for amino acids (AA) and purines to estimate the flow of microbial protein at the duodenum. Statistical analyses were done in R using a linear random regression model with DM content as fixed effect, cow and growth x farmer as random intercepts and with a growth x farmer random slope. Results given below are per 10% units increase in DM content of grass-clover silage. The absorption of AA in the small intestine was increased (P = 0.03) with 5.59 g/kg DM intake. The increased absorption was caused by a higher small intestinal digestibility of AA (1.27 g/100g AA, P = 0.03) and a higher flow of AA in the duodenum (5.63 g/kg DM intake, P = 0.08). The higher flow of AA in the duodenum derived from both a higher flow of microbial AA (2.12 g/kg DM intake, P = 0.06), and a lower true rumen degradation of AA from the silage (−4.04 g/100g AA, P = 0.04). In conclusion, the MP concentration in grass-clover silage can be improved by pre-wilting to a higher DM content before ensiling.