Many commercial bird diets are made with soy products that contain phytoestrogens (i.e., plant compounds that have weak agonist activity at estrogen receptors), but the effects of these compounds on bird physiology and behavior are largely unknown. The primary phytoestrogens present in soy are the isoflavones genistin and diadzin, which have been shown to affect reproductive measures in many taxa. Two groups of wild-caught male Dark-eyed Juncos (Junco hyemalis) were fed a diet either made with water-washed soy protein (soy(+)) or made with soy protein that had been alcohol-washed to extract isoflavones (soy(-)). Both groups exhibited a photoperiodic response to long days. Plasma luteinizing hormone (LH) concentrations increased within the first week of long day (LD) exposure for both groups, and over the course of the experiment LH was higher in the soy(+) group, although concentrations for both groups were lower than have been reported in free-living juncos. The rate of cloacal protuberance (CP) growth was significantly affected by diet, with the soy(-) birds beginning to increase their CPs about a week faster than soy(+) birds after exposure to LD. There was no group difference in food intake, fat score, body mass, or behavioral measures during the study or in testis weight at the end of the study. Although effects of dietary phytoestrogens detected were subtle (i.e., rate of CP growth), those investigating subtle effects of hormonally active substances (e.g., endocrine disruptors) or environmental cues affecting the reproductive axis in songbirds may want to consider eliminating phytoestrogens from their experimental diets.