Most real networks are characterized by connectivity patterns that evolve in time following complex, non-Markovian, dynamics. Here we investigate the impact of this ubiquitous feature by studying the Susceptible-Infected-Recovered (SIR) and Susceptible-Infected-Susceptible (SIS) epidemic models on activity driven networks with and without memory (i.e., Markovian and non-Markovian). We show that while memory inhibits the spreading process in SIR models, where the epidemic threshold is moved to larger values, it plays the opposite effect in the case of the SIS, where the threshold is lowered. The heterogeneity in tie strengths, and the frequent repetition of connections that it entails, allows in fact less virulent SIS-like diseases to survive in tightly connected local clusters that serve as reservoir for the virus. We validate this picture by evaluating the threshold of both processes in a real temporal network. Our findings confirm the important role played by non-Markovian network dynamics on dynamical processes.