Vegetable soybeans are harvested when the seeds are green and fill the pod completely, and are usually boiled in pods or shelled for 5 to 15 minutes before eating. The objective of this research was to characterize the change in quality attributes of vegetable soybean when subjected to 6 boiling times (0, 5, 10, 15, 20, and 30 min) and two cooking methods (shelled or in pods). Soluble sugars, texture, color, iron, and trypsin inhibitor activity was analyzed. We observed a change in all variables measured when samples were boiled, except for the content of raffinose + stachyose. Sucrose levels increased during the first 5 minutes of boiling, and then decreased linearly, with a steeper slope for the samples boiled shelled as compared to those boiled in pods. Glucose + fructose levels decreased when the samples were initially cooked, and then remained stable; however, the levels of glucose + fructose were higher for samples boiled in pods than those shelled. Hardness levels increased when samples were initially subjected to boiling and then decreased linearly, but no significant effect of cooking method (in pods or shelled) was observed. Hunter's “-a/b” value for seed color constantly increased with cooking time, and samples cooked in pods had more intense green color at any time compared to samples boiled shelled. Iron content of soybean seeds decreased with cooking time, but no statistical differences were observed for samples boiled in pods and shelled. Trypsin inhibitors were rapidly deactivated with boiling, and no further change in activity was observed with boiling time or cooking method. In conclusion, boiling vegetable soybeans for 5 minutes in pods is recommended as the best cooking method, because the samples retain a desired green color, while hardness, sucrose, and iron levels remain high, and antinutritional factors are fully deactivated.