Background Using native wildflowers for restoring marginal lands has gained considerable popularity. Establishment of wildflowers can be challenging due to several environmental factors. Restoring the microbial community in degraded habitats can potentially result in the native plant performance and habitat restoration. This study was conducted to investigate the impact of native soil microbes and seeding depth on germination of south Texas native wildflowers. Two wildflower species, Ratibida columnifera (Nutt.) (Mexican Hat) and Verbesina encelioides (Cav.) (cowpen daisy), were treated with microbial wash extracted from native soils, and germination rate was recorded for 14-day period. We further analyzed the growth, biomass allocation, and root colonization by mycorrhizal fungi in these two plants growing them in a plant growth chamber for 6 weeks. To determine the impact of seeding depth, we planted the seeds of the two plant species at 2-cm, 6-cm, and 12-cm depth and monitored germination and plant growth. Results The two species responded differently to the seeding depth and microbial wash treatments. Microbial wash treatment resulted in higher germination rate in R. columnifera compared to control, while it did not have any impact on V. encelioides seed germination. While microbial treatment did not influence the total biomass, it had a significant impact on the biomass allocation in both the plant species. R. columnifera seeds germinated at both 2-cm and 6-cm depth and did not germinate at 12 cm, while the V. encelioides seeds germinated only at 2 cm and did not germinate at 6-cm or 12-cm seeding depth. Conclusions While our results are species specific, our results indicate that native soil microbes can potentially improve the seed germination and growth of wildflowers. Our results also indicate the importance of specific seeding depth when sowing wildflower seeds for habitat restoration.