Objectives: The effect of dietary protein intake on bone mineral density (BMD) has not been explained in patients with spinal cord injury (SCI). In this study, we looked at the relationship between BMD and higher protein intake in patients with SCI while controlling for possible confounders. Methods: Patients with SCI, who were referred to the Brain and Spinal Cord Injury Research Center between November 2010 and April 2012, were included in the study. In total, the dietary intakes of 103 patients were assessed by 24–hour dietary recall interviews. We used dual-energy X-ray absorptiometry to measure BMD in the femoral neck, trochanter, intertrochanteric zone, hip, and lumbar vertebras. Results: Eighty-six men and 17 women participated in this study. Protein intake was negatively associated with the BMD of lumbar vertebrae (p = 0.001, r = –0.37 for T-score and p = 0.030, r = –0.24 for Z-score). The BMD of lumbar vertebrae were negatively associated with intake of tryptophan, isoleucine, lysine, cysteine, and tyrosine (p = 0.007, 0.005, 0.009, 0.008, and 0.008 for T-score, respectively). Higher intakes of threonine, leucine, methionine, phenylalanine, valine, and histidine were related to a lower BMD of lumbar vertebrae (p = 0.006, 0.010, 0.009, 0.010, 0.009, and 0.008 respectively for T-scores). Conclusions: We found that high protein intake led to a lower BMD of lumbar vertebrae in patients with SCI after controlling for confounders including demographic and injury-related characteristics and calcium intake. No relationship between higher amino acids intake and BMD of the femur and hip was detected. Intake of alanine, arginine, and aspartic acid were not related to BMD.