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Understanding the transgenerational dynamics of gut microbiota in black soldier fly larvae (BSFL) is essential for optimizing their performance on novel waste substrates in industrial settings. In this study, a wild-type BSF population was divided into six sub-lines and reared over four generations: one line on standard chicken feed (CF) and five on a novel plant-based diet (WIL), four of which were subjected to selection for increased larval size. Despite a shared genetic origin, sub-lines exhibited divergent trajectories in both larval weight and gut bacterial composition. Larval weight increased up to the second (G2) or third (G3) generation but declined sharply at generation four (G4) across all lines. Parent-offspring regressions revealed low narrow-sense heritability, suggesting limited genetic contribution to larval weight variation. Gut microbiota analysis revealed that early developmental stages were most sensitive to generational shifts, with the transition from G3 to G4 showing the strongest changes in community structure. Core species, including multiple <i>Enterococcus</i> spp. and <i>Providencia rettgeri</i>, were consistently detected across all lines, diets, and generations. Most of these were classified as "Neutral" or "Above" in the Sloan Neutral Model, suggesting functional and survival importance regardless of selection regime or substrate. Deviations from neutrality were more pronounced in WIL-fed lines, consistent with intermediate disturbance dynamics, while CF-fed lines exhibited fewer deviations under low-disturbance, stable conditions. Notably, growth-associated taxa, such as <i>Bacillus</i> and <i>Paenibacillus</i>, peaked in G2 to G3 but declined at G4, whereas immune modulatory taxa, such as <i>Klebsiella</i>, increased in abundance. These trends indicate a shift from growth-promoting to digestion- and resilience-oriented microbial strategies under prolonged dietary stress. The stochastic emergence of distinct microbial patterns across sub-lines underscores the plastic and adaptable nature of BSFL gut microbiota. Recognizing this plasticity emphasizes the need to maintain large, genetically and microbially diverse BSF populations, which is critical for preserving functional stability and supporting long-term adaptation when utilizing novel or suboptimal substrates in industrial production.IMPORTANCEThe black soldier fly is rapidly gaining recognition globally as a key agent in circular bioeconomy for its ability to convert diverse organic waste into high-value products. However, the long-term stability and resilience of its gut microbiota on novel, low-cost diets remain poorly understood. This study addressed that knowledge gap by tracking transgenerational changes in larval gut microbial communities over four generations, using a single population reared on a novel diet, both with and without selection for larval size. Despite a shared genetic background, different sub-lines developed distinct microbiota and growth patterns, with early developmental stages showing the greatest sensitivity to generational microbial shifts. Initial increases in certain bacterial groups were followed by community restructuring by the fourth generation, indicating a dynamic but unstable microbial response to prolonged dietary stress. These findings highlight the importance of preserving microbial and genetic diversity when breeding black soldier flies for industrial use. Understanding how host-microbiota responses shift across generations is essential for sustaining performance and ensuring resilience in large-scale black soldier fly production systems.