The overuse of chemical fertilizers deteriorates soil quality, and the application of organic amendments has been proposed as an alternative to mineral fertilizers. This study aimed to investigate the effects of organic amendment types on soil properties, the soil microbiome, and tomato growth. Tomato seedlings were grown in soils applied with ten fertilizer treatments, including a no fertilization control, a chemical fertilization control, and eight organic amendment treatments. Compared with the chemical fertilization treatment, the application of manure compost significantly increased the shoot dry weight of tomato plants. In addition, manure compost and tea seed meal remarkably increased soil organic matter (SOM) in comparison with the no fertilization and chemical fertilization treatments. Moreover, manure compost significantly increased soil-exchangeable K and Mg. The application of neem cake and manure compost significantly increased both bacterial diversity and richness. The relative abundance of Lysinibacillus was significantly positively related to the shoot and total dry weights of tomato plants, and its relative abundance was positively influenced by SOM and soil-exchangeable K. Overall, the manure compost used in this study can increase SOM, soil-exchangeable K and Mg, and the relative abundance of Lysinibacillus, consequently promoting tomato growth.