Forests host important plant biodiversity. Nevertheless, due to climate change and human disturbances, the floristic quality of forest ecosystems is degraded. Greek peri-urban forests biodiversity is threatened by anthropogenic activities such as forest fragmentation, pollution, garbage, etc. Measurement of biodiversity status and the floristic quality assessment can be used to estimate the degree of forest degradation caused by anthropogenic disturbances. In this study, we compared and evaluated six forest ecosystem types in the peri-urban forests of Thessaloniki, northern Greece, by using Shannon’s biodiversity index as well as and α and β diversity Sørensen indices. Furthermore, we recorded the prevailing anthropogenic disturbances and compared the plant families and the ruderal species appearing in each forest ecosystem. Finally, the average conservatism value (C value) of the plant species found in each ecosystem was determined in order to calculate the ecosystem floristic quality index. Analysis of the results showed that the floristic and ecological parameters tested greatly vary among ecosystems. Broadleaf forests of higher altitude hosted the greatest biodiversity, and the higher floristic quality index and plant conservation value. On the contrary, most disturbances and most ruderal species were recorded in ecosystems of lower altitude, adjacent to the city (Pinus brutia forest and Maqui vegetation), the least disturbed ecosystems were found in the steep slopes (Castanea sativa forest). Most ruderal species found belonged to the Asteraceae and Rosaceae families. Accessibility and attractiveness of stands were positively correlated with disturbances. Insufficient management, lack of protection measures, and littering removal contribute to the increase in the level of disturbance.