Debate on differences between milk from grazing and non-grazing cows has not addressed the effects that standard processing may have on milk digestibility. In this study, raw milk from grazing organic (ORG) and non-grazing conventional (CONV) herds was adjusted to 0 and 3.25% fat and processed as follows: raw skim milk (Sr) was HTST (Sp) or UHT (Su) pasteurized, and raw whole milk (Wr) was homogenized (Whr), HTST pasteurized (Wp), homogenized and HTST pasteurized (Whp), or homogenized and UHT pasteurized (Whu). Milk then underwent 60 min of gastric digestion (NaCl, pepsin, and HCl; pH 1.5) and 120 min of intestinal digestion (ID) (K₂HPO₄ buffer, bile salts, pancreatin, and NaOH; pH 7.0). Samples were evaluated using a particle size analyzer, SDS-PAGE, nitrogen analysis, FFA titration, and GC-FID. Adjusting milk to gastric conditions resulted in large clots; Sr and Sp formed the largest clots, ORG > CONV (P < 0.05), while Whu had the smallest. Within 15 min, clots had decreased in size (nonfat > whole milk) and the caseins hydrolyzed to large and medium-sized peptides. Transition to intestinal conditions further decreased particle sizes (whole > skim) and only medium and small peptides remained at 15 min ID. Skim and ORG Whu samples contained only small peptides as early as 15 to 60 min ID. Proteins were 85 to 94% digested at 120 min ID. Addition of lipase in the ID phase resulted in rapid release of free fatty acids (FFA) during the first 15 min and then slowed as FFA accumulated. Homogenized whole milk released the most FFA and contained highest levels of saturated FA (8:0, 10:0, 12:0, and 14:0). Compared with ORG milk, CONV whole milk released more FFAs and contained higher levels of C16:0 and 18:0. ORG whole milk contained higher levels of 6:0 14:1, 16:1, 18:1 trans, 18:2 isomers (conjugated linoleic acid, CLA), and 18:3 (P < 0.05) before and after processing than CONV milk. Although some minor differences existed between the milk from grazing ORG and confined CONV cows during in vitro digestion, milk from both sources responded similarly to standard processing treatments and were highly digestible, important information for health conscious consumers.