As the world population keeps increasing, ammonia-based fertilizers like urea are essential to provide food security. However, the current fertilizer industry is based on fossil fuel feedstock (mainly natural gas), making the production process CO2 emission-intensive. More specifically, besides the CO2 emitted during the process, the CO2 captured in urea is also released into the atmosphere after the fertilizer is applied to agricultural soils. Thus, positioning the fertilizer industry among the top four industrial emitters globally. Hence, in order to meet the target of limiting global warming to 1.5 ºC and achieve net-zero emissions by 2050, it is necessary to strengthen the carbon mitigation efforts in the current fertilizer industry. This can be achieved in different ways, such as using renewable biofuels and implementing technologies that can lead to zero/negative CO2 emissions. For that reason, the present study presents pathways to achieve a more environmentally friendly fertilizer production process. An overall analysis is performed if negative emissions can be achieved by replacing different fractions of natural gas (used as both feedstock and fuel) with biogas and biomethane and by capturing and storing the CO2 emitted from the process using chemical solvents as activated MDEA and MEA. The results obtained from the study revealed that negative emissions in fertilizer plant can be achieved by retrofitting an existing ammonia plant with a MEA based CO2 capture system (with a carbon capture rate of 90%) for the SMR burner flue gas, and by introducing 50% of biogas in the feedstock (alongside Natural gas), and 75% of biogas in the SMR burner fuel (alongside Natural gas). This initial approach would result in net negative emissions from urea's production and application and require approximately 0.5 kg of biogas per kg of urea produced in this case. Furthermore, the equivalent energy intensity for the negative emission urea plant would be 0.32% and 3.37% lower compared to the fossil fuel-based case without/with CCS, respectively. Ultimately, it is even possible to produce approximately 6% more urea product by replacing a particular fraction of natural gas with biogas. The reason for this increased production is due to the surplus of carbon dioxide by the introduction of biogas. It can be used along with the ammonia product going to storage in the fossil fuel-based case, where there was not enough CO2 to keep the feedstock molar ratio at the urea plant's inlet.