jats:titleAbstract</jats:title>jats:pThe early stages of community development influence longer‐term establishment of species, traits, and ultimately ecosystem function. How this process varies with small‐ and large‐scale abiotic and biotic conditions is poorly studied in microbes. Here, we tested how different spatial scales influenced the rate at which taxonomic and functional composition of microbial communities changed over time in lake sediments, and whether these changes occurred synchronously across different environments given the same initial communities. We manipulated the small‐scale environment by creating sediments with different terrestrial organic matter (t‐OM) quantity and quality, and placing these in two lakes differing in trophic status to vary the large‐scale environment. We found that archaeal and bacterial communities, but not fungi, became taxonomically dissimilar over 2 months despite being derived from the same initial leaf material, primarily because of small‐scale environmental conditions. Sediment t‐OM quantity consistently explained changes in community composition both temporally within mesocosms and spatially between mesocosms in different lakes. Archaea, bacteria, and fungi also varied by up to 10 times in how quickly they changed, providing among the first evidence in the same study system that they respond differently over time to abiotic and biotic conditions. Finally, functional composition was influenced by both small‐ and large‐scale environmental conditions, with genes involved in t‐OM decomposition showing some of the largest changes in abundance after 1 yr. Our study highlights that future changes to both sediments and lake waters can modify how sediment microbial communities develop with consequences for important ecosystem functions like carbon cycling.</jats:p>