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The intrinsic value of soil to national, regional and local agroecological and economic productivity in sub-Saharan Africa is not adequately manifest in financial planning and decision making, challenging long-term sustainability as that resource degrades. While efforts to internalize the external costs of soil erosion in monetary units are available in the literature, we offer an alternative approach based on emergy synthesis, which enumerates the value of soil based on the environmental work required to produce it rather than based on surveys or derived pricing techniques. Emergy synthesis integrates all flows within a system of coupled economic and environmental work in common biophysical units (embodied solar energy or solar emjoules - sej), facilitating direct comparisons between natural and financial capital. Insight into long-term sustainability of human economic production and its basis in natural capital stocks is achieved via a suite of emergy-based indices. Our objective was to provide context for the magnitude of soil erosion losses within the larger resource basis of the Kenyan economy at three scales. Our results suggest that erosion losses at the national scale (4.5E21 sej/yr) are equal in magnitude to national electricity production or agricultural exports (equivalent to $ 390 million annually or 3.8% of GDP). This significant hidden, long-term cost is magnified in the selected district economies. In particular, in Nyando district (a densely populated rural district in western Kenya) we estimate that soil erosion represents over 14% of total emergy flows. The soil intensity of agriculture (SIA = agricultural yield/soil loss, both in emergy units) of Nyando (2.25) illustrates a severely marginalized agricultural sector in comparison with the nation as a whole (SIA = 7.56) or other nations (SIAUSA = 81.9, SIABrazil = 15.6). Soil loss measurements across land uses typical in western Kenya allowed emergy evaluation of differential costs and benefits;soil loss represented between 12 and 62% of total emergy use (subsistence agriculture SIA = 8.13, communal rangeland SIA = 1.62). By quantifying the ecological costs of soil erosion in units directly comparable with flows in other sectors of the economic system, we provide a baseline measure of sustainability against which appropriate investment (i.e., scaled to problem magnitude, targeted to hot-spots) in soil conservation may be evaluated.