Background The association of plant-based diets and biomarkers of bone, insulin, and inflammation is still unclear. Objectives We investigated the associations between biomarkers of bone, insulin, and inflammation and three plant-based diet indices: an overall plant-based diet index (PDI); a healthy plant-based diet index (hPDI); and an unhealthy plant-based diet index (uPDI). Methods We included 178 elderly subjects who referred to health centers in Tehran. Blood and urine samples were collected to measure osteocalcin. The Human C-telopeptide of type ? collagen (u-CTX-I), highly sensitive C-reactive protein (hs-CRP), parathyroid hormone (PTH), 25(OH) D, and insulin resistance and sensitivity. We created an overall PDI, hPDI, and uPDI from semi-quantitative food frequency questionnaire (FFQ) data. Results Dietary groups of Vegetables (r = .15, p = .03), nuts (r = .16, p = .03), dairy (r = .25, p = .001), eggs (r = .27, p < .001), red meat, and animal products (r = .25, p = .001) were directly correlated with osteocalcin. Refined grains were also had a positive association with serum insulin concentration (r = .14, p = .04). PTH levels are inversely associated with PDI score (beta = -0.18, p = .01). Also, serum insulin concentration was negatively associated with PDI score (beta = -0.10, p = .04). Urine CTX-1 levels were significantly associated with hPDI score (beta = -0.06, p = .04). u-CTX-1 levels are inversely associated with uPDI score. This significance did not change with the adjustment of the confounders (beta = -0.28, p < .001). Conclusions More adherence to PDI and hPDI and less in uPDI may have a beneficial effect on biomarkers of bone, inflammation, and insulin thus preserving chronic diseases.