Many biological populations are subject to periodically changing environments such as years with or without fire, or rotation of crop types. The dynamics and management options for such populations are frequently investigated using periodic matrix models. However the analysis is usually limited to long-term results (asymptotic population growth rate and its sensitivity to perturbations of vital rates). In non-periodic matrix models it has been shown that long-term results may be misleading as populations are rarely in their stable structure. We therefore develop methods to analyze transient dynamics of periodic matrix models. In particular, we show how to calculate the effects of perturbations on population size within and at the end of environmental cycles. Using a model of a weed population subject to a crop rotation, we show that different cyclic permutations produce different patterns of sensitivity of population size and different population sizes. By examining how the starting environment interacts with the initial conditions, we explain how different patterns arise. Such understanding is critical to developing effective management and monitoring strategies for populations subject to periodically recurring environments.