The process of mixing and reaction is a challenging problem to understand mathematically. Although there have been successes in describing the effective properties of mixing and reaction under a number of regimes, process descriptions for early times have been challenging for cases where the structure of the initial conditions is highly segregated. In this paper, we use the method of volume averaging to develop a rigorous theory for diffusive mixing with reactions from initial to asymptotic times under highly segregated initial conditions in a bounded domain. One key feature that arises in this development is that the functional form of the averaged differential mass balance equations is not, in general, scale invariant. Upon upscaling, an additional source term arises that helps to account for the initial configuration of the reacting chemical species. In this development, we derive the macroscopic parameters (a macroscale source term and an effectiveness factor modifying the reaction rate) defined in the macroscale diffusion-reaction equation and provide example applications for several initial configurations.