Root-associated compartments, including rhizosphere soil, rhizoplane soil, and the endosphere, are found to harbor distinguished bacterial populations and community composition, but how microbiome in these rhizo-compartments are affected by edaphic variables remains largely unknown. Goethite is a prevalent crystalline iron (hydr)oxide mineral of the soil matrix and strongly interact with microbial communities. The objective of our study was to determine how goethite (α-FeOOH) amendment assemble bacterial communities in the rhizo-compartments of Maize (Zea mays. L). Using sequencing of microbial 16S ribosomal RNA gene amplicons, we revealed that goethite amendment into soil enriched Actinobacteria and depleted Proteobacteria in all rhizo-compartments. Also, goethite enlarged the differences in the alpha diversity (Chao) between rhizo-compartments, with much lower mean diversity in the endosphere and rhizoplane compared with rhizosphere soil, indicating a higher selection of the microbiome assemblage. This was supported by beta Nearest Taxon Index (βNTI > + 2), indicating that changes in environmental conditions progressively increase the strength of selection. It suggests that variable selection (a deterministic process) was the dominant process influencing the microbial assembly in soil amended with goethite. According to the distance-based linear modeling (distLM), the assemblage of bacterial communities in the rhizosphere compartments was regulated by specific edaphic variables, with the major contributors being goethite (62%), total C (52%), soil pH (50%), and FeOM (25%). Stabilization of rhizosphere C in the presence of goethite would be the selective step for its accessibility and consequent microbial community. For instance, the keystone microorganisms, e.g., Pseudomonas, had more negative links within the goethite added co-occurrence network, indicating its mutual exclusions and outcompete other microbes in C/nutrients limited conditions. Thus, goethite narrows the composition of rhizosphere mainly due to “gate selection” effects on rhizodeposits, which limited microbial penetrance into inner-compartments, consequently assemble the rhizosphere bacterial community via deterministic process.