The invention relates to methods for extracting a kerogen-based product from subsurface (oil) shale formations. These methods rely on chemically modifying the shale-bound kerogen using a chemical oxidant so as to render it mobile. The oxidant is provided to a formation fluid in contact with the kerogen in the subsurface shale. A mobile kerogen-based product which includes the organic acids is withdrawn from the subsurface shale formation and processed to isolate the organic acids contained therein. In one embodiment, the mobile kerogen-based product is treated such that at least a portion of the organic acids form a separate phase from the mobile kerogen-based product to isolate the acids. The organic acids may further be extracted from the mobile kerogen-based product using an organic extraction fluid.