<p>While the mechanisms that govern disease emergence and spread among hosts are increasingly well-described, the mechanisms that promote parasite diversity within-hosts, affecting host outcomes and spillover potential, have been comparatively understudied. Furthermore, while attention has been paid to the effects of increasing temperatures on disease systems, the effects of environmental variability have been left underexplored, despite rising climatic variability. To investigate the impacts of environmental variability on parasite co-occurrence within-hosts, we analysed a model of within-host population dynamics wherein two parasites indirectly compete through the host’s immune response. We simulated the model under constant, demographically stochastic, environmentally stochastic, and demographically and environmentally stochastic conditions, and analysed the viability and longevity of non-equilibrium parasite co-occurrence. We found that environmental stochasticity increased the viability and longevity of parasite co-occurrence, suggesting that thermal variability arising from climatic change and as a physiological trait may promote parasite diversity within ectotherms and help explain bats’ propensity to support diverse communities of parasites. Further, we found that under certain conditions, the transmissibility of co-occurring parasites can surpass the transmissibility of single parasites, suggesting that thermal variability may increase the transmissibility of co-occurring parasites.</p>