Currently there are no unified AACC methods for whole wheat milling. Commercial and laboratory scale millings are different in the grinding apparatus used, number of streams, and way of bran-flour reconstitution. In the current study, we aim to examine whole wheat flour (WWF) from laboratory milling methods and to compare them with those from commercial mills, from both analytical and bake perspectives. Four WWF samples were prepared with several different laboratory mills, including a Bühler laboratory pneumatic mill (model MLU-202), a Thomas Wiley cutting mill, a combined hammer mill and roller stand, and a Hosokawa grinder. Three commercial WWF samples were obtained from a commercial mill plant, representing coarse, medium, and fine particle sizes. All WWF samples above are milled from the same hard red spring wheat. Ro-tap, farinograph, bread, and cookie baking were tested and compared. Ro-tap results showed that laboratory milled WWF samples are closer to medium, fine or ultrafine WWF as that of commercial flour. Farinograph data validated that the finer the flour is, the higher water absorption the flour has; and for the above 7 flour samples, the absorption ranges from 66.6% to 69.8%. However, it is interested to find a trend that the finer the flour is, the shorter stability the flour has; and stability of the above 7 flour samples ranges from 6.2 to 13.9 min. Bread bake was finished at fixed water absorption and mixing time, of which data is partially consistent with trend of farinograph data. The finer the flour sample was, the drier the doughs was, and the more strength the dough had. Neither coarsest nor finest flour demonstrated highest bread volume or height. And the finer particle size deteriorated the bake quality more than coarse particle size did. It is the medium/slightly fine flour that performed best under the current bake formulation/method. The flour samples were also baked as cookies, of which spread factor (SF) is positively correlated with bran particle size in general. The lowest SF was 49.3 and highest SF was 71.0. As a result, whole wheat milling can be optimized for best bake performance and successful quality evaluation of certain commercial WWF can be obtained by laboratory mill methods, too.