This work is an endeavour on the subject of the Critical Success Factors imposed by Human Resources, in the process of reforms, under the context of New Public Management, particularly, as this applies in the Greek Public Sector and more specifically in the cases of ISO implementation. The fundamental issues it attempts to elucidate are the Human Resources policies that must be applied, so that employees become an integral element for the successful implementation of any introduced reforms. Many scholars have pointed out the gap in literature regarding the effect of New Public Management (NPM) reforms on the human factor. Moreover, in the current Greek reality, in the context of the economic recession and the debt crisis, where public administration reforms are mandatory, the thorough examination of the vital issues, pertaining to Human Resources, consists a major priority. The qualitative research method applied with the employees of the reformed organisations has further aspired to ponder and determine what really matters during the transformational process from the employees’ point of view. The conclusions we have reached underpin the importance of Human Resources motivational factors in the reform process, taking into consideration that the employee is the catalyst for any change effort.  Some of those factors were found to be also part of the ISO concept per se, thus, their implementation would boost the employees’ morale, while others must be carefully analysed, planned and implemented by all the stakeholders to further facilitate the change process. We have to bear in mind that, especially under the current dire economic environment, quality reforms could be a challenge, as they combine fiscal discipline and at the same time aspire to increase the employees’ and citizens’ satisfaction. This study goes further to suggest that, the implementation of ISO reforms could help all the participants, provided that the decision makers take into serious consideration the Critical Success Factors outlined herewith, that have been extracted from a survey conducted pertinent to our research. This study focused on the reforms/ISO process as implemented by the Intermediate Managing Authority of the Ionian Islands. Further research on the implications from the implementation of NMP doctrines on Human Resources should be conducted in other Greek governmental organisations, in order to reaffirm the results and possibly enhance the suggested model. Conclusively, our ultimate target is to assist decision makers and encourage them to utilise the arguments depicted, towards the successful implementation of NPM doctrines