Mangrove ecosystems contribute significantly to coastal stability, providing essential services like carbon sequestration and storm protection. The rehabilitation of mangroves in Indonesia is essential to restore ecological functions disrupted by coastal development. This study aims to compare the ratios of organic matter—carbon (C), nitrogen (N), and phosphorus (P)—in the soils of natural and rehabilitated mangroves in Benoa Bay, Bali. The research was conducted across eight plots in natural and rehabilitated mangrove forests, with soil samples collected using an auger at depths ranging from 0 to 100 cm. Organic matter analysis was performed using the loss on ignition (LOI) method for soil organic carbon (SOC), the FIA method for total nitrogen (TKN), and the colorimetric persulfate digestion method for total phosphorus (TP). The results indicate that rehabilitated mangroves have lower total organic carbon (1.1±0.5%) and higher total nitrogen content (0.07±0.02%) compared to natural mangroves. Total phosphorus content is also lower in rehabilitated areas (0.010±0.003%), possibly due to increased clay content that binds phosphorus in the soil. Several parameters are closely related to organic matter, including bulk density, soil type, oxidation-reduction potential (ORP), pH, and dissolved oxygen (DO) in pore water, as well as the structure of mangrove stands, such as tree and seedling density, stem diameter, canopy cover, and the health condition of mangroves. Variations in organic matter content and C:N ratios suggest that rehabilitated mangrove ecosystems have not yet reached the same stability as natural ecosystems, as reflected in altered biogeochemical cycles and nutrient availability. Therefore, ongoing efforts are needed to ensure a more comprehensive recovery in the mangrove rehabilitation process. These findings highlight the need for targeted interventions in mangrove rehabilitation programs to ensure long-term nutrient balance restoration, which is essential for optimizing carbon storage and resilience to climate change in tropical coastal ecosystems.