Nowadays one of the most important decisions in safety issues in Brazilian Oil and Gas industry is that it’s necessary to shut down plant because one specific failure or required maintenance in protection system makes influence on risk level. Most of time, experienced operators make decisions based on their background despite carrying out a risk analysis to support their decision. Therefore in so many cases, refinery plants work on catastrophic risk level due to subjective decisions. In order to improve the operator decision, a specific methodology was established to apply risk assessment using PRA (Preliminary Risk Analysis), LOPA (Layer of Protection Analysis) and FTA (Fault Tree Analysis) in order to check risk level or layer of protection availability. By this way, as the first step, the Preliminary Risk Analysis will be carried out in order to qualify risk and mainly define consequences severity. The second step will carry out the LOPA in order to find out the failure probability of all layers of protection and without one of those layers of protection which requires maintenance or even failure. In addition, when is necessary to check that contingency systems availability FTA will be carried out? In the first case, it is possible to substitute the layer of protection for another in order to keep risk on acceptable level. In the second case, it is necessary to check if contingency system is available and assess if consequence gets worse or keeps on the same level. In both cases, the final risk will be assessed and compared with the previous one defined on PRA. In case of risk, it is unacceptable that the final decision will shut down plant. The refinery study case will be shown as an instance of such methodology.