Environmental fluctuations have important consequences in the organization of ecological communities, and understanding how such a variability influences the biodiversity of an ecosystem is a major question in ecology. In this paper, we analyze the case of two species competing for the resources within the framework of the neutral theory in the presence of environmental noise, devoting special attention on how such a variability modulates species fitness. The environment is dichotomous and stochastically alternates between periods favoring one of the species while disfavoring the other one, preserving neutrality on the long term. We study two different scenarios: in the first one species fitness varies linearly with the environment, and in the second one the effective fitness is re-scaled by the total fitness of the individuals competing for the same resource. We find that, in the former case environmental fluctuations always reduce the time of species coexistence, whereas such a time can be enhanced or reduced in the latter case, depending on the correlation time of the environment. This phenomenon can be understood as a direct consequence of Chesson’s storage effect.