Reforestation with exotic species has often been used in arid and semiarid areas to restore degraded ecosystems. However, the effects of these plantations on soil biodiversity are still under debate. In the present study, we aimed to evaluate the long-term impacts (>60 years) of exotic plantations with Acacia cyclops and Pinus halepensis on soil biodiversity in an insular arid ecosystem of high ecological value. To do so, we study soil quality and soil arthropod communities in patches of vegetation under uniform edaphoclimatic conditions. Soil quality assessment was carried out by developing an ad-hoc Soil Quality Index (SQI) across seven sites, including two plantations (Pinus or Acacia), two degraded areas with a low cover of native species, and three sites with a high cover of native species. Whole organism community DNA (wocDNA) metabarcoding and barcoding were used to analyse key soil arthropod groups (Coleoptera, Acari and Collembola) recognized as habitat quality and biodiversity indicators. Our findings show that exotic plantations improved soil quality compared to degraded sites, with a considerable increase in the organic carbon pool, macronutrients and microbiological activity (SQI = 0.53 f 0.12 vs. 0.29 f 0.06). This improvement did not reach the values recorded in soils with a high cover of preserved native flora (SQI = 0.65 f 0.12), with some exceptions. Richness of mesofauna and Coleoptera was lower in degraded areas (4.4 f 1.6 and 0.4 f 0.7, respectively) followed by exotic plantations (9.5 f 2.6 and 1.2 f 0.9) and permanent native vegetation (14.1 f 5.5 and 2.2 f 1.8). Soil quality significantly explained up to 52 % and 17 % of the variance in the richness of mesofauna and Coleoptera, respectively. While exotic plantations appear to prevent further land degradation in terms of soil quality, multivariate analysis shows that the structure of soil arthropod communities, particularly in Pinus plantations and to a lesser extent in Acacia plantations, differs significantly from that of soils in ecosystems with remnant native flora. These results highlight the need for a careful balance between biodiversity conservation and soil health management, especially in areas susceptible to desertification.