Dry bean utilization by the food industry can be increased by developing value-added processing applications. The goals of this research were to evaluate (1) the effect of milling method on the physical, chemical and functional properties of whole black bean flour and its fractions and (2) the effect of removing soluble phenolic compounds on the functional and rheological properties of black bean protein isolates. Black bean was milled with five laboratory mills [cyclone mill, hammer mill, stone mill (fine, medium, coarse), disc mill (fine, coarse), and centrifugal mill (10,000 or 12,000 rpm and 250, 500, 1000 μm aperture screen)] and the resulting flours were evaluated for their physical, chemical and flow properties of bulk samples and particle size fractions. Whole black bean flour and cotyledon flour were subjected to phenolic extraction and protein isolation, resulting in protein isolates with and without soluble phenolics. Solubility, wettability, dispersibility, water binding capacity, foam capacity and stability, emulsification capacity, and gelation properties of protein isolates were evaluated. Variation in milling method produced flours with significantly different flour characteristics. Geometric mean size of whole bean flour was negatively correlated with starch damage (r = -0.92), L* (r = -0.94), angle of repose (r = -0.94), and angle of slide (r = -0.80 to -0.90) and positively correlated with moisture (r = 0.72), and loose bulk density (r = 0.72). Milling method and particle size interaction was significant on characteristics of black bean flour fractions. Particle circularity of flour fractions had a negative correlation of r = -0.93, r = -0.81, r ≈ -0.95, and r = -0.94 with L*, angle of repose, angle of slide and compact density, respectively. Particle circularity had a positive correlation of r = 0.93 and r = 0.89 with average minimum particle size and loose bulk density, respectively. The removal of soluble phenolic compounds improved the brightness, solubility, wettability, dispersibility, foaming capacity, foaming stability, emulsion capacity, emulsion stability and gelling properties of protein isolates. These findings will help food manufacturers to process black bean ingredients using different mill settings to achieve different functionalities depending on the consumer requirements.