Healthy forests are essential to human life because they provide food, energy, and other benefits including carbon sequestration. The objective of this study was to assess the forests health status in Mediterranean ecosystems, specifically, arid to semi-arid. Four forest reserves directed by Royal Society for the Conservation of Nature, Jordan were evaluated. Plant health indicators [(gas exchange (photosynthesis, stomatal conductance, transpiration), chlorophyll, middy stem water potential (Ψsmd), relative water content], regeneration, lichens, plant disease, as well as soil variables (respiration CO2-C, electrical conductivity (EC), pH, microorganisms’ abundance) were measured. The Ψsmd values in those semi-arid/arid ecosystems were within the normal ranges (−0.3 to −1.3 MPa) in spring but was under extreme water stress (−1.6 to −5.3 MPa) in summer in three reserves. Similarly, gas exchange variables reduced by 25%–90% in summer (compared to spring) across the studied forests. Although the regeneration (seedling per 1000 m2) was higher than 100 in two forest (Ajloun and Dibbeen), the number of seedlings in hiking sites was extremely low in both forests. Soil health indicators reveled that soil respiration CO2-C were higher than 25 mg kg−1 in two forests [Ajloun, Dibbeen, (except hiking zone)]. The mean soil saprophytes (number g−1) ranged from 86 to 377 across the forests reserves. In addition, the mean arbuscular mycorrhizal fungi (spores 100g−1 soil) was between 350 and 877. Soil EC was consistently optimal (less than 0.5 dS m−1) and pH was slightly basic (7.5–8.3) across the reserves. The results revealed that the fluctuation of rainfall and anthropogenic pressures (grazing, hiking) led to partial forest degradation. When forests (Dana Biosphere Reserve) received 81 mm annual precipitation, Ψsmd values in Juniperus phoenicea at summer ranged from −4.4 to −5.3 MPa, regeneration and lichens were less than 20 per 1000 m2, and several trees were dead after infected with soil and air borne pathogens including wilt diseases and die back. Intensive hiking activities (Dibbeen forests, tourism area) and heavy grazing (Yarmouk frosts) reduced regeneration, lichens and soil respiration. Interestingly, the native species had better water relations (RWC, Ψsmd) and gas exchange performance than the introduced species. Overall, it is better to grow native species, and exclude anthropogenic pressure on the territory of introduced species. The conservation programs must persist to sustain several native historical forest trees including Juniperus phoenicea (>600 year old), Quercus ithaburensis (>500 year old), and Pinus halepensis (>100 year old) at Mediterranean semi-arid forests. Keywords: soil health; forest tree diseases; climate change; physiological status; semi-arid ecosystems.