A certification in accordance with ISO 14 001 and EMAS allows the impact of economic activities on ecosystems to be understood and assessed, as well as environmental goals and objectives to be set. The effects of environmental management systems (EMS) largely depend on how companies decide to use them after certification. In this regard, the author explores issues, related to the use of ISO 14 000 and EMAS standards for improving the environmental safety of companies. The methodology is presented in the form of an environmental standardisation model and various levels of the company environmental certification. The importance of environmental education of employees and a positive organisational climate is explained. However, the introduction of environmental management systems does not always lead to improved environmental performance of companies. Some companies focus on formal criteria. Nevertheless, EMS, environmental auditing and the principles of ISO 14 000 can help companies reduce their negative impact on the environment and increase their competitiveness. In a situation of uncertainty, the organisational climate, especially the attitude of employees towards the environment and environmental values, is of a priority importance for the implementation of the EMS objectives. Problems, associated with an ambiguous interpretation of standard requirements, were identified. It is recommended to pay attention to the creation of a positive organisational climate for successful environmental certification. In addition, there is a need for a more accurate assessment of the environmental activity effectiveness with a clear formulation of the requirements to standards and a control over their implementation.