This study discussed project methods most applied for NGO''s projects focusing on the accountability challenges faced by project managers. It further analysed how in practice managers are dealing with the impact of project actions and the results that would legitimate NGO''s purpose. It was evidenced in practice that management methodologies are applied to fulfil the organization strategic needs therefore project management knowledge is assumed as a semi structure basis and can be adjusted once the work is justified. Accordingly, a flexible approach relies on the project management method that is highly influenced by the expertise of the organization staff. As a conclusion, it was evidenced in practice that NGO''s projects carry particular aspects and expectations over project accountability therefore management methodologies are adapted and complemented by novel approaches. In order to investigate it, a case study was carried on a well recognized Institute that works with environmental issues and some novel approaches were found out and discussed.