We assess the ionospheric scintillation occurrence on Global Navigation Satellite Signals (GNSSs) over the Mediterranean sector under the rising phase of the current solar cycle. To the scope, we leverage on a network of three Ionospheric Scintillation Monitor Receivers (ISMRs), being part of the electronic Space Weather upper atmosphere (eSWua: eswua.ingv.it) system (Pica et al., 2021). Such ISMRs are located in Lampedusa Island (Italy, Lat: 35.52 - Lon: 12.63), Chania (Crete, Greece, Lat: 35.52, Lon: 24.04) and Nicosia (Cyprus, Lat: 35.18 - Lon: 33.38). To our knowledge, this is the first thorough assessment of the scintillation patterns in the Southern Mediterranean sector, aimed at depicting how small-scale irregularities form in the area and potentially affect the GNSS-based positioning and related application and services. We analyse the period from January 2021 to December 2023, reporting that the bulk of the scintillation occurrence is due to small-scale irregularities forming in the southernmost area of the field of view of the network. Irregularities of such a scale are formed during the evolution of the Rayleigh-Taylor instability featuring the Equatorial Plasma Bubbles (EPB), which may spill-over in the field of view (FoV) of the receivers, i.e. at low elevation angles in the southernmost azimuthal range. As observations at low elevation angles are subject to multipath mimic weak to moderate scintillation conditions, we focus exclusively on severe amplitude scintillation occurrence ( S4  > 0.7) in the azimuthal range 110°-250°, w.r.t the FoV of the receivers, reaching then down to the Saharian ionosphere. To further confirm the nature of the detected GNSS scintillation occurrence, we compare the results with the Swarm Level-2 Ionospheric Bubble Index (IBI) evaluated within the same period. In the context of the April 2023 geomagnetic storm, a worst-case scenario is also documented, illustrating the potential impact of ionospheric disturbances associated with EPBs in the Southern Mediterranean area.