No clear consensus on the role of higher protein intakes has emerged, in spite of many decades of research. Protein unambiguously increases urinary calcium losses, which is completely attributable to the dietary acid load imposed by metabolism of sulfur containing amino acids into acid equivalents. Although alternate dietary sources of fixed acid cause demineralization of bone and apparent osteoporosis, this effect has not been consistently observed for protein, suggesting opposing, beneficial effects on bone. Specifically, protein may improve bone health through improving calcium absorption, increasing total circulating insulin-like growth factor 1 or by improving lean body mass which in turn increases bone growth. Although the notion of competing positive and negative pathways has been articulated theoretically, statistical mediation models of this “dual pathways” relationship have not been employed to quantify these relationships. In a cross-sectional investigation of postmenopausal women, protein intake is positively related to bone mineral density of the lumbar spine following adjustment for an accompanying negative effect mediated by the sulfur containing fraction of protein. In growing rats, an analogous and complementary pattern emerged: A negative association of protein intake with bone strength was suppressed by an opposing, positive effect of protein mediated by insulin-like growth factor 1. A second animal study assessed the influence of protein source on bone strength and bone mineral content of growing rats consuming isoenergetic, isonitrogenous diets. The influence of protein source was completely mediated by the corresponding changes in lean body mass. A randomized, controlled trial indicated a higher protein diet preserved bone density during weight loss compared to a conventional, MyPyramid based diet; however the protein diet also contained more calcium. A mathematical model of calcium availability in this trial suggested that this additional dietary calcium was not sufficient to explain differences in calcium accrual between groups unless calcium availability was also improved in the higher protein diet. Also, within this study, urine calcium (a surrogate of the diet acid load) exhibited a negative association with bone density change, in spite of its positive association with protein intake. The striking consistency of a dual pathway model across populations and experimental models lends credence to the notion that dietary protein may hold a positive or negative effect on bone health, depending on other factors in the diet. Specifically, we find support that the sulfur containing amino acid induced dietary acid load holds negative effects that may be opposed by positive influences of insulin-like growth factor 1, calcium availability or lean body mass. On average, this effect is probably null or too small to be of clinical importance. The effect may be of public health relevance, however, if the diet can be manipulated in order to uncouple positive and negative pathways. If correct, the dual pathway model predicts higher protein intakes will have modest benefits on bone health in the context of adequate calcium intake, selection of protein sources lower in sulfur amino acids or ample intake of fruits and vegetables to buffer the dietary acid load.