The theory of quantum jump trajectories provides a new framework for understanding dynamical phase transitions in open systems. A candidate for such transitions is the atom maser, which for certain parameters exhibits strong intermittency in the atom detection counts and has a bistable stationary state. Although previous numerical results suggested that the “free energy” may not be a smooth function, we show that the atom detection counts satisfy a large deviations principle and, therefore, we deal with a phase crossover rather than a genuine phase transition. We argue, however, that the latter occurs in the limit of an infinite pumping rate. As a corollary, we obtain the central limit theorem for the counting process. The proof relies on the analysis of a certain deformed generator whose spectral bound is the limiting cumulant generating function. The latter is shown to be smooth so that a large deviations principle holds by the Gärtner–Ellis theorem. One of the main ingredients is the Krein–Rutman theory, which extends the Perron–Frobenius theorem to a general class of positive compact semigroups.