Morphological plasticity is an adaptive response to heterogenous environments when a fitness advantage is conferred. Larval sea urchins, for example, increase individual fitness in dilute feeding environments by elongating their feeding structure. Morphological plasticity for larval sea urchins is also coupled with significant shifts in the associated bacterial community, but whether this response occurs before, during, or following the expression of plasticity is unclear. Using the sea urchin Lytechinus variegatus, we define the temporal pattern of the associated bacterial community throughout the expression of morphological plasticity. From prefeeding through plasticity, we observed that L. variegatus larvae exhibit a four-stage successional pattern and the relatedness of the larval-associated bacterial community directly reflects morphological plasticity and does so prior to expression of the environmental-specific morphology. Based on the structure of the larval-associated bacterial communities, the expression of morphological plasticity correlates short-arm larvae deviating from the microbial trajectory of pre-plastic siblings. Taken together, these data suggest that a holobiont may exhibit shifts in the associated bacterial community corresponding with the environmental variation in absence or anticipation of morphological plasticity.