The annual fertilizer use would increase by 50% in India to increase crop production by 20% from current level to feed 1.7 billion people by 2050. While increasing crop production by 20% to feed the growing population remains a priority, the fertilizer industry has also prioritized climate-smart agriculture to minimize the impact on the environment. Without the reduction in emission intensity, increases in productivity cannot be sustainable over the long term. Reconciling the goals of increasing food demands together with reduced GHG emission from increased fertilizer use requires adoption of good practice guidelines of fertilizer use. It is thus important to consider which technologies and practices can be applied that meet not only adaptation needs, but also mitigation needs. Thus, management practices need to be identified to better utilize fertilizer, while at the same time safeguarding the environment. Therefore, this book chapter aims to discuss the effect of natural and management factors that influence the biochemical and physical processes that determine GHGs emission from fertilizer use.