Traditionally, epidemiological studies have focused on understanding the dynamics of a single pathogen, assuming no interactions with other pathogens. Recently, a large body of work has begun to explore the effects of immune-mediated interactions, arising from cross-immunity and antibody-dependent enhancement, between related pathogen strains. In addition, ecological processes such as a temporary period of convalescence and pathogen-induced mortality have led to the concept of ecological interference between unrelated diseases. There remains, however, the need for a systematic study of both immunological and ecological processes within a single framework. In this paper, we develop a general two-pathogen single-host model of pathogen interactions that simultaneously incorporates these mechanisms. We are then able to mechanistically explore how immunoecological processes mediate interactions between diseases for a pool of susceptible individuals. We show that the precise nature of the interaction can induce either competitive or cooperative associations between pathogens. Understanding the dynamic implications of multi-pathogen associations has potentially important public health consequences. Such a framework may be especially helpful in disentangling the effects of partially cross-immunizing infections that affect populations with a pre-disposition towards immunosuppression such as children and the elderly.