<p>The gut–brain axis represents a bidirectional communication system disrupted in obesity. Evidence suggests associations between gut microbiota composition and brain function and eating behaviour, as well as between dysregulated brain networks and dietary choices and metabolic regulation. In this review, we examine how obesity affects both components of this axis and explore physical activity as a modifiable factor related to microbial composition and brain network connectivity. We discuss compositional alterations in the gut microbiota associated with obesity, including reduced microbial diversity and altered short-chain fatty acid production. On the brain side, dysregulation of large-scale functional networks, particularly the salience network, central executive network, and default mode network, is linked to impaired inhibitory control and disinhibited eating patterns. Despite promising evidence connecting physical activity with improvements in both gut microbiota and brain connectivity, observational and interventional studies show inconsistencies regarding temporal dynamics and causal relationships. To examine these questions, we augment our review with longitudinal data from 702 participants assessed across three timepoints using random-intercept cross-lagged panel models, which distinguish stable individual differences from dynamic within-person variation. Our findings indicate temporal associations in which physical activity precedes shifts in connectivity in attention-related networks, which subsequently precede alterations in gut microbiota diversity, consistent with predominantly brain-to-gut temporal patterns with network specificity. Taken together, these results highlight a potential role of physical activity in modulating both brain connectivity and microbial composition, with possible relevance for obesity treatment.</p>