Third sector organizations are organizational structures that contribute to the countries social welfare. This type of organizations requires their audiences support and understanding in order to accomplish their organizational objectives and, to obtain such support, they must communicate in a transparent form with their audiences. Transparency must be understood as a third sector organizations ethical duty with a view to announce their audiences not only detailed information about the use of financial resources but also to keep them informed about their actions, decisions and daily behaviors. Third sector organizations must manage their transparency and best practices not as designed action within a logistical or merely operational plan, but as the core idea of a strategic plan that allows them to create bonds of trust with strategic audiences such as: collaborators, donors, volunteers, government, other third sector organizations and society. When the audiences notice that a third sector organization puts their transparency and best practices into practice as an ethical and voluntary attitude for making visible and explaining each one of their actions, decisions, projects, profits and results, they will not hesitate to participate with it and offer their unconditional support. Comprehensive communication plays a fundamental role in the transparency strategic management of the third sector organizations, since it is through it that the audiences are able to know in detail the organization actions. Owing to, currently, digital media own a great reach, third sector organizations transparency and best practices must be communicated using digital media in a proper form. That is, organizations must not only design strategies to strengthen their transparency, but they also must communicate them with their audiences. With that said, the objective of this research was to analyze and to compare through a content analysis the comprehensive communication level in digital media owned by the third sector organizations from Mexico and Spain with NGO certification accredited to communicate their transparency and best practices to their audiences via their website and official social media: Facebook and Twitter. The third sector organizations sample was of 104 Spanish organizations and 104 Mexican organizations. This research was performed through a quantitative content analysis. Such analysis is digital and it was carried out in the official website and in two social media: Facebook and Twitter. It is a cross-sectional research, since the information gathering was performed during the period January-August, 2020. The research stages were: definition of the sample, definition of variables, information coding and analysis and interpretation of results. The study categories were determined from the nine transparency and best practices principles of Lealtad y Confío foundation; indications based on international standards recommended by the ICFO (International Committee on Fundraising Organizations). The main findings were that the communication level in the Spanish third sector organizations was better than in the Mexican organizations; however, both organizations have the challenge to efficiently communicate their transparency using digital media. Although it is true that Spain owns a better level of transparency and best practices comprehensive communication in digital media compared to Mexico, it has merely focused in taking advantage of its website, leaving the advantages of social media, Facebook and Twitter, aside.