Osteopenia, sarcopenia, and increased vascular stiffness are common in patients with chronic kidney disease-mineral bone disorder (CKD-MBD) with protein energy wasting and can lead to worse clinical outcomes. We investigated the potential moderating role of the lean tissue index (LTI) in the relationship between bone microarchitecture and vascular stiffness in dialysis naïve patients with stage 5 CKD. Bioimpedance spectroscopy for evaluating LTI, lumbar spine dual energy X-ray absorptiometry for determining the trabecular bone score (TBS), and arterial applanation tonometry measurements for the central augmentation index, at a heart rate of 75 beats/minute (cAIx75), were simultaneously performed in 117 consecutive patients. A hierarchical regression analysis was conducted to assess the moderating effect of LTI on the relationship between TBS and cAIx75 after adjusting for age and sex. The effect of the interaction between LTI and TBS on cAIx75 was statistically significant (p = 0.030), demonstrating that the cAIx75 tends to decrease more, with the joint effect of LTI and TBS. In the separate analyses, the interaction effect was significant only in women (p = 0.048) and the group of diabetes (p = 0.042). Our study suggests that the evaluation of changes in body composition, bone health, and vascular stiffness needs to be performed simultaneously in patients with advanced-stage CKD. Further research in patients with different stages of CKD warranted to generalize and apply our results to patients in other stages.