We present a quantitative analysis of phosphorus (P) flows that characterize the food production-consumption system metabolism in a low-income, food, and phosphorus deficient country, using Comoros, a small African island state, as an example from the year 2000 to 2011. The data were interpreted in terms of the connections between crop production, livestock breeding, human consumption, and soil stock, using the substance flow analysis (SFA) model. We found that the total P input into Comoros totaled 132.37 t in 2000 and 270.60 t in 2011, whereas the total P output totaled 567.40 t in 2000 and 702.29 t in 2011. Farmers in Comoros are cropping with little or no P input, resulting in a soil P deficiency; it varied from 435.03 t in 2000 to 431.69 t in 2011. In addition, the Phosphorus Use Efficiencies (PUEs) of plant and animal production in Comoros were 131.80% and 14%, respectively, in 2011. This is the first SFA of a small island state, and the lack of a closed P loop is a major issue for the country in terms of P security and this has not changed between 2000 and 2011. This study proposes crucial solutions for improving the PUE through recycling and reusing animal manure, human excreta, and household solid organic waste.