To modulate isoflavone aglycone composition within a soy functional food, soy ingredients were processed and evaluated in a soy bread system intended for clinical trials. A soy flour/soy milk mixture (SM) was boiled, fermented, steamed, or roasted prior to dough preparation. The isoflavone compositions of five processed SM and their corresponding breads combined with and without β-glucosidase-rich almonds were examined using HPLC. Isoflavone malonyl-glucosides (>80%) were converted into acetyl and simple glucoside forms (substrates more favorable for β-glucosidase) in steamed and roasted SM. Their corresponding breads had isoflavones predominately as aglycones (∼75%) with soy-almond bread with steamed SM being more consumer acceptable than roasted. Isoflavone composition in soy bread was stable during frozen storage and toasting. A suitable glycoside-rich soy bread (31.6 ± 2.1 mg aglycone equiv/slice) using unprocessed SM and an aglycone-rich soy-almond bread (31.1 ± 1.9 mg aglycone equiv/slice) using steamed SM were developed to evaluate fundamental questions of isoflavone bioavailability in clinical trials.