Ibiza (Eivissa) is one of the main Balearic Islands in the western Mediterranean. Recent studies have highlighted the genetic distinctiveness of present-day Eivissans within the region and suggested it could be attributed to the genetic drift caused by recent demographic events. Whether this distinctiveness emerged from a differential demographic history, or rather from a bias for sampling in a small geographic region such as Eivissa, remains an open question, together with the understanding of the functional consequences of demography in the island. In order to clarify these questions and further characterize the distinctiveness of Eivissa within the Balearic and Mediterranean context, we generated whole exome sequences for 31 and 20 individuals from Eivissa and Menorca respectively, a subset of which were also genotyped with the Human Origins array. Our results show that Eivissans present signs of putatively recent genetic isolation that are shared to a lesser extent with Menorca such as more and longer runs of homozygosity and high numbers of intra-population shared IBD segments. Regarding the functional consequences of recent demography, although Eivissans do not present an excess of deleterious alleles or homozygotes comparing to other populations, genetic drift seems to have increased the allele frequencies of neutral and deleterious variants, which can have various medical implications.