Despite its crucial role in plant health and nutrient dynamics, the spatial heterogeneity of the rhizosphere microbiome has often been overlooked. This study employed a mini-rhizobox approach to investigate spatiotemporal variations in the rhizosphere of pepper plants, analyzing an extensive dataset of 2,185 samples. Our results revealed high spatial variability in bacterial communities within the rhizosphere of individual plants, as indicated by both alpha- and beta-diversity. Stochastic processes were identified as the primary drivers of bacterial community assembly at adjacent points, particularly in secondary roots, whereas deterministic processes exerted more influence in main roots and their junctions with secondary roots. Correspondingly, only 22.3% of generalist ASVs followed skewed Gaussian distributions along root depth. These findings highlight randomness in bacterial taxa along roots. Nonetheless, bacterial richness, as indicated by the log₁₀ transformation of detected ASVs, showed a strong negative correlation with the dominance rate (R² = 0.994). Additionally, a distance-decay relationship was observed, with increasing divergence between the main and secondary roots. These insights advance our understanding of rhizosphere microbial ecology, clarifying the mechanisms underlying the randomness within rhizosphere microbiome.