Microbial community assembly is a series of ecological filtering mechanisms that determine the composition of microbial communities.  While the importance of broad and local level factors on microbial communities has been reasonably well studied, this work is often limited to static observations and neglects to consider temporal variation.  Since temporal variation is an important determinant of community assembly and determines the relative importance of community assembly filters, this represents a key knowledge gap.  Due to their close associations with seasonal variation in plant growth and fitness, arbuscular mycorrhizal (AM) fungi are useful groups for assessing the importance of temporal dynamics in microbial community assembly.  We tested how seasonal variation (spring vs. summer), plant life history stage (vegetative vs. flowering), and host plant species (Baptisia bracteata var. leucophaea & Andropogon gerardii) influenced AM fungal spore community assembly.  AM fungal spore community temporal dynamics were closely linked to plant host species and life history stage.  While AM fungal communities demonstrated strong turnover between the spring (e.g., higher sporulation) and late summer (e.g., higher diversity), the strength and direction of these changes was modified by host plant species.  Here we demonstrate the importance of considering temporal variation in microbial community assembly, and also show how plant-microbe interactions can modify seasonal trends in microbial community dynamics.