This thesis is devoted to the development of a nonperturbative quantum field theoretical approach to flavour physics, with special attention to cosmological applications. Neutrino flavour oscillation is nowadays a fairly well-established experimental fact. However, the formulation of flavour oscillations in a relativistic field theoretical framework presents non-trivial difficulties. A nonperturbative approach for building flavour states has been proposed by Blasone, Vitiello and coworkers. The formalism implies a non-trivial physical vacuum (called flavour vacuum), which might act as a source of Dark Energy. Furthermore, such a vacuum has been recognized as the effective vacuum state arising in the low energy limit of a string theoretical model, D-particle Foam Model. In the attempt of probing the observable phenomenology of the D-particle foam model, a simple toy model (two scalars with mixing `a la Blasone & Vitiello on a adiabatically expanding background) has been studied, proving that the flavour vacuum might behave as Dark Energy under certain assumptions. The first work presented in this thesis represents a development of this approach. A more realistic model is considered, which includes two flavoured Dirac fermions on a generic Friedmann-Robertson-Walker universe. In this framework we show that the flavour vacuum presents different features, which are incompatible with Dark Energy. Motivated by this discrepancy, we next embark on the analysis of a simple supersymmetric model in flat spacetime (free Wess-Zumino), proving that the bosonic component of flavour vacuum acts as Dark Energy, whereas the fermionic as a source of Dark Matter. Finally we develop a new method of calculation that open the way to a nonperturbative extension of these results for interactive theories.