Two important goals of sustainable agriculture are food production and preserving and improving soil health. The soil organic carbon content is considered an indicator of soil health. The evaluation of the methods to increase the soil organic carbon content in long-term experiments is usually carried out without considering its environmental effects, (e.g., CO2–C soil emission). This study hypothesized that sandy soils have a low carbon storage potential, and that the carbon accumulation in the soil is accompanied by increased CO2–C emissions into the atmosphere. The study was carried out as a long-term fertilization experiment in Central Poland using a rye monoculture. The changes in the soil organic carbon content (SOC), CO2–C emissions from soil, and plant yields were examined for two soil treatments: one treated only with mineral fertilizers (CaNPK) and one annually fertilized with manure (Ca + M). Over the 91 years of the experiment, the SOC content of the manure-fertilized treatment increased almost two-fold, reaching 10.625 g C kg−1 in the topsoil, while the content of the SOC in the soil fertilized with CaNPK did not change (5.685 g C kg−1 in the topsoil). Unlike mineral fertilization, soil manuring reduced the plant yields by approximately 15.5–28.3% and increased the CO2–C emissions from arable land. The CO2–C emissions of the manured soil (5365.0 and 5159.2 kg CO2–C ha−1 in the first and second year of the study, respectively) were significantly higher (by 1431.9–2174.2 kg CO2–C ha−1) than those in the soils that only received mineral fertilizers (3933.1 and 2975.0 kg CO2–C ha−1 in the first and second year of the study, respectively). The results from this experiment suggest that only long-term fertilization with manure might increase the carbon storage in the sandy soil, but it is also associated with higher CO2–C emissions into the atmosphere. The replacement of mineral fertilizers with manure, predicted as a result of rising mineral fertilizer prices, will make it challenging to achieve the ambitious European goal of carbon neutrality in agriculture. The increase in CO2–C emissions due to manure fertilization of loamy sand soil in Central Poland also suggests the need to research the emissivity of organic farming.