Ideally, you should try soy isoflavones only if you ovulate irregularly or not at all. Don't use them if you have any health issues that could be made worse. Though, there are many stories where soy isoflavones have helped some women, they do the same thing that Clomid does. However, many experts believe, the type of oestrogen in soy actually makes endo worse which is why you should avoid it. Minimizing your intake of oestrogen from outside sources, such as commercially raised animal foods could be more beneficial. Eat soy foods such as tofu which are rich in plant oestrogens and seem to block more harmful forms of oestrogen. Few studies also proved that Dietary isoflavones may in fact reduce the risk of endometriosis. So theres no confirmed data available.
How about Agnus castus, which is also known as natures Clomid? It works on your prolactin levels which then support ovulation and the luteal phase which relies on hormones to sustain a pregnancy once an embryo has developed.