The maternally inherited bacterium Wolbachia is well known for spreading in natural populations by manipulating the reproduction of its arthropod hosts, but can also have mutualist effects that increase host fitness. In mosquitoes and Drosophila some Wolbachia strains can lead to an increase in survival of virus-infected insects, and in most cases this is associated with reduced accumulation of the virus in host tissues. We investigated if the Wolbachia strain wSuz, which naturally infects Drosophila suzukii, is able to confer protection against Drosophila C virus and Flock House virus in different host genetic backgrounds. We found that this strain can increase host survival upon infection with these two viruses. In some cases this effect was associated with lower viral titres, suggesting that it confers resistance to the viruses rather than allowing the flies to tolerate infection. Our results indicate that, in D. suzukii, the antiviral protection provided by Wolbachia is not correlated to its density as found in other Drosophila species. This study demonstrates a phenotypic effect induced by wSuz on its native host which could explain its maintenance in natural populations of D. suzukii.