This work focuses on the use of green roof as a modified shallow vertical flow constructed wetland for greywater treatment in buildings. Different design parameters such as substrate (perlite or vermiculite), substrate depth (15 cm or 25 cm), and plant species (Geranium zonale, Polygala myrtifolia or Atriplex halimus) were tested to determine optimum selection. In addition, the application of a 40% recirculation rate was applied during last month of the experiment to quantify the efficiency of pollutants removal. The experiment was conducted for a period of 12 months under typical Mediterranean climatic conditions in Lesvos island, Greece. Results showed that green roofs planted with Atriplex halimus and filled with 20 cm of vermiculite had the best COD (91%), BOD (91%), TSS (93%) and turbidity (93%) average removal efficiencies. In contrast, significant lower removals were observed when the substrate depth was decreased to 10 cm (60–75%). Green roof vegetation had significant impact on TN removal as the average TN concentration decreased from 6.5 ± 1.8 mg/L in the effluent of unplanted systems to 4.9 ± 2.7 mg/L in the effluent of green roofs planted with Atriplex halimus. The recirculation of a portion of the effluent in the influent had as a result a significant improvement of turbidity, organic matter and (especially) nitrogen removal. For example, BOD removal in green roofs planted with Atriplex halimus and filled with 20 cm of perlite increased from 76% to 92%, while TN removal in green roofs planted with the same plants and filled with 20 cm of vermiculite increased from 56% to 87%. Overall, the operation of green roofs as modified vertical unsaturated constructed wetlands seems a sustainable nature-based solution for greywater treatment and reuse in urban areas.