Plant restoration strategies are ubiquitously employed for the purposes of soil and water conservation and ecological improvement in forest ecosystems. Despite N and temperature being acknowledged as pivotal factors affecting plant restoration outcomes, their effects on soil fertility, microbial communities, and shrub biomass remain underexplored, particularly in the loess hilly regions of China. Here, we examined the growth patterns and nutrient acquisition abilities of three shrub species, Periploca sepium, Amorpha fruticosa, and Vitex negundo, along with the attendant alterations in soil properties and microbial community composition under controlled greenhouse conditions. Specifically, we imposed three levels of N fertilization (200, 400, and 600 kg ha−1; designated as N1, N2, and N3, respectively) and temperature regimes (18–23, 25–30, and 32–37 °C; labeled T1, T2, and T3, respectively). The results indicated a significant interplay between the combination of N fertilization and temperature significantly affecting shrub growth. Optimal growth conditions, as evidenced by the highest dry biomass accumulation, were identified as N3T1 for A. fruticosa, N1T1 for P. sepium, and N2T2 for V. negundo, with these conditions differentially influencing roots, stems, and leaves. Furthermore, soil microorganisms also responded significantly to the N fertilization and temperature. However, this was largely dependent on shrub species and soil nutrients. For A. fruticosa under N3T1 conditions, Actinobacteria and Basidiomycota abundances correlated strongly with soil C, N, and P contents, while leaf N uptake significantly correlated with the structure of both bacterial and fungal communities. For P. sepium at N1T1, Acidobacteriota was dominant in response to soil N and C, while leaf C uptake and leaf and stem N uptake positively correlated with bacterial and fungal communities, respectively. For V. negundo at N2T2, Chloroflexi had the greatest abundance, responding to the greatest variation in soil N and C, while its stem N uptake was significantly related to the structure of the fungal communities. Thus, our findings underscored the intricate interplay between abiotic factors, shrub growth, soil fertility, and microbial community dynamics, providing insights into the optimization of plant restoration efforts in ecologically sensitive regions.