Spontaneous collapse models aim to resolve the measurement problem in quantum mechanics by considering wave-function collapse as a physical process. We analyze how these models affect a decaying flavor oscillating system whose evolution is governed by a phenomenological non-Hermitian Hamiltonian. In turn, we apply two popular collapse models, the QMUPL and the CSL models, to a neutral meson system. By using the equivalence between the approaches to the time evolution of decaying systems with a non-Hermitian Hamiltonian and a dissipator of the Lindblad form in an enlarged Hilbert space, we show that spontaneous collapse can induce the decay dynamics in both quantum state and master equations. Moreover, we show that the decay property of a flavor oscillating system is intimately connected to the time (a)symmetry of the noise field underlying the collapse mechanism. This (a)symmetry, in turn, is related to the definition of the stochastic integral and can provide a physical intuition behind the Itō/Stratonovich dilemma in stochastic calculus.