Progress in breeding of intermediate wheatgrass (Thinopyrum intermedium), a perennial grain with environmental benefits, has enabled bran removal. Thus, determination of optimum milling conditions for production of refined flours is warranted. This study explored the effect of tempering conditions on intermediate wheatgrass flour properties, namely composition, color, solvent retention capacity, starch damage, and polyphenol oxidase activity. Changes in flour attributes were evaluated via a 3 × 3 × 2 factorial design, with factors targeting moisture (comparing un-tempered controls to samples of 12% and 14% target moisture), time (4, 8, and 24 h), and temperature (30 and 45 °C). All investigated parameters were significantly affected by target moisture; however, samples tempered to 12% moisture showed few differences to those tempered to 14%. Similarly, neither tempering time nor temperature exerted pronounced effects on most flour properties, indicating water uptake was fast and not dependent on temperature within the investigated range. Lactic acid retention capacity significantly correlated with ash (r = −0.739, p < 0.01), insoluble dietary fiber (r = −0.746, p < 0.01), polyphenol oxidase activity (r = −0.710, p < 0.01), starch content (r = 0.841, p < 0.01), and starch damage (r = 0.842, p < 0.01), but not with protein (r = 0.357, p > 0.05). In general, tempering resulted in flour with less bran contamination but only minor losses in protein.