This paper aims to understand about how uncertainty emerges in the innovation process. Since uncertainty is embedded in the innovation process, to understand how uncertainty emerges in the process one needs to understand how innovation process unfolds over time. Since an innovation process involves various resource recombination activities occurring in several phases, to understand how innovation process unfolds one needs understand “how do various resource recombination activities occur over time for the creation of novelty?” This knowledge would enable us to understand the conditions under which vital activities of resource recombination can/cannot be undertaken and coordinated as well as would allow us to understand the underlying decisions made by the innovators for their efficient undertaking and coordination. This paper investigates the innovation process in two companies through performing qualitative study. The innovation processes are analysed in the light of a conceptual model developed based on the Dubois’ (1994) End-product related activity structure model, Håkansson’s (1987) “ARA model” and Goldratt’s (1997) “Critical chain concept”. The findings suggest that uncertainty emerges in the innovation process in a cycle of interaction with resource void, activity void and actors’ limited cognition due to lack of knowledge, undue optimism, and rationally justified reason for disregarding information. Accordingly, a great deal of compromises is made while undertaking the activities.