The Posidonia oceanica decline due to climate change and other anthropogenic pressures, such as chemical pollution, is well known in the scientific community. However, a comprehensive study of the full content of the organic micropollutants found in this significant seagrass has not yet been carried out. Second, an eco-friendly extraction procedure that does not require a large sample, preserves the seagrass’s ecological integrity and functions, and follows green-chemistry principles, is lacking. These information gaps represent the aims of this study. For this purpose, trials with diverse simple and affordable extraction methods to detect one of the most ubiquitous contaminants (polycyclic aromatic hydrocarbons or PAHs) were conducted. As a result, the use and validation of a polytron homogenizer and an ultrasonic bath were proposed for the extraction of priority PAHs from tissues of P. oceanica and marine sediments, respectively. Tissues (leaves and rhizomes) of P. oceanica and sediment samples were collected, extracted, and subjected to a thorough analysis, i.e., target, suspect, and unknown screenings, using gas chromatography coupled to high resolution mass spectrometry (GC-Q-Orbitrap MS). Target analysis revealed seven priority parent-PAHs, whilst during the suspect screening, four PAH-derivatives and three other parent-PAHs were tentatively identified. In the additional third unknown analysis, 11 structures, several with concerning toxicity, were also tentatively identified. Numerous of the identified compounds showed elevated detection frequency in the environmental samples, even reaching 100%, such as the cases of the parent-PAHs (naphthalene, phenanthrene and retene), some PAH-derivatives, one UV stabilizer, and plastic additives along with pesticides. The methods proposed here should be considered for future monitoring of P. oceanica, as well as the three-way analytic approach (target, suspect and unknown), to obtain a more real and accurate idea of the organic micropollutants content in the environment.