Abstract In vitro procedures using flasks have been used for simulating nutrient utilization by pigs. However, these procedures are time-consuming and laborious and require a number of flasks and filter crucibles. The objective of this study was to develop an in vitro procedure using DaisyII incubator for simultaneous analysis of multiple samples. In a conventional in vitro procedure, 10 mg of pepsin in step 1 and 50 mg of pancreatin in step 2 are used for each flask containing 1 g of feed sample. In a preliminary experiment, 24 samples each in R55 bags were digested in a jar of DaisyII incubator with 24 times the quantity of buffer solution and enzymes of the conventional flask procedure. In the preliminary experiment, greater crude protein (CP) digestibility values were observed in the DaisyII incubator procedure compared with the conventional flask procedure. To determine optimum enzyme doses in the in vitro ileal disappearance (IVIDDaisy) procedure using the DaisyII incubator, 3 doses of pepsin (10, 7.5, and 5 mg/sample in step 1) and 3 doses of pancreatin (50, 37.5, and 25 mg/sample in step 2) were tested in a 3 × 3 factorial arrangement for 11 test ingredients. The quantity of buffer solution and enzymes in a jar was increased proportionally with the number of samples. The 11 test ingredients were barley, copra meal, corn, corn distillers dried grains with solubles, corn gluten feed, corn gluten meal, palm kernel meal, rice bran, soybean hulls, soybean meal, and wheat bran. The in vitro ileal disappearance (IVIDflask) of CP in the 11 ingredients was determined using the conventional flask procedure. The sum of square of deviation between IVIDflask of CP and IVIDDaisy of CP was the least when 5 mg pepsin/sample in step 1 and 37.5 mg/sample in step 2 were used (IVIDflask of CP, % = 14.4 + 0.81 × IVIDDaisy of CP, %; r2 = 0.748). On the other hand, the determination coefficient was the greatest when 10 mg pepsin/sample in step 1 and 50 mg/sample in step 2 were used (IVIDflask of CP, % = 2.5 + 0.93 × IVIDDaisy of CP, %; r2 = 0.878). In conclusion, the in vitro procedure using a DaisyII incubator can be used for estimating ileal digestibility of protein in multiple samples simultaneously for pigs.