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Rhizosphere microbial communities are important components of the soil-plant-atmosphere continuum in paddy field ecosystems where they contribute to nutrient cycling and rice productivity. However, the rhizosphere microbial sensitivity to anthropic soil disturbance across plant growth stages remains little investigated. Here, we tracked the effects of long-term (> 25 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three growth stages (tillering, panicle initiation and booting). Our results reveal that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with growth stage and that the bacterial and archaeal community differed in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at the panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at the tillering and booting stage. However, the effect of growth stage on microbial sensitivity to long-term inorganic fertilization was more strongly pronounced for bacterial than archaeal community. Furthermore, our results reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across growth stages. Hence, our study brings new insights on rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization across growth stages in field-grown rice. By identifying one of the critical rice growth stages during which rhizosphere microbial communities are highly sensitive to inorganic fertilization, our results open new avenues for developing appropriate strategies in microbiome engineering to mitigate biotic and abiotic stress and improve crop yields.