Mabira Central Forest Reserve (CFR), one of the biggest forest reserves in Uganda, has increasingly undergone encroachments and deforestation. This chapter presents the implications of a range of forest management options for carbon stocks in the Mabira CFR. The effects of forest management options were reviewed by comparing above-ground biomass (AGB), carbon, and soil organic carbon (SOC) in three management zones. The chapter attempts to provide estimates of AGB and carbon stocks (t/ha) of forest (trees) and SOC using sampling techniques and allometric equations. AGB and carbon were obtained from a count of 143 trees, measuring parameters of diameter at breast height (DBH), crown diameter (CW), and height (H) with tree coordinates. It also makes use of the Velle (Estimation of standing stock of woody biomass in areas where little or no baseline data are available. A study based on field measurements in Uganda. Norges Landbrukshoegskole, Ås, 1995) allometric equations developed for Uganda to estimate AGB.The strict nature reserve management zone was noted to sink the highest volume of carbon of approximately 6,771,092.34 tonnes, as compared to the recreation zone (2,196,467.59 tonnes) and production zone (458,903.57 tonnes). A statistically significant relationship was identified between AGB and carbon. SOC varied with soil depth, with the soil surface of 0–10 cm depth registering the highest mean of 2.78% across all the management zones. Soil depth and land use/cover types also had a statistically significant effect on the percentage of SOC (P = 0.05). A statistically significant difference at the 95% significance level was also identified between the mean carbon stocks from one level of management zones to another. Recommendations include: demarcating forest boundaries to minimize encroachment, enforcement of forestry policy for sustainable development, promote reforestation, and increase human resources for efficient monitoring of the forest compartments.