Given the frequent overlap between biological plant invasion and ecological restoration efforts it is important to investigate their interactions to sustain desirable plant communities and modify long-term legacies both above- and below-ground. To address this relationship, we used natural reference, invaded and created vernal pools in the Central Valley of California to examine potential changes in direct and indirect plant effects on soils associated with biological invasion and active restoration ecosystem disturbances. Our results showed that through a shift in vegetation composition and changes in the plant community tissue chemistry, invasion by non-native plant species has the potential to transform plant inputs to soils in vernal pool systems. In particular, we found that while invasive plant litter decomposition was driven by seasonal and interannual variability, associated with changes in precipitation, the overall decomposition rates for invasive litter was drastically lower than native species. This shift has important implications for long-term alterations in plant-based inputs to soils in an amplifying feedback to nutrient cycling. Moreover, these results were independent of historic active restoration efforts. Despite the consistent shift in plant litter decomposition rates and community composition, we did not detect associated shifts in below-ground function associated with invasion by non-native plants. Instead, soil C:N ratios and microbial biomass did not differ between invaded and naturally occurring reference pools but were reduced in the manipulated created pools independent of invasion levels. Our results suggest that while there is an observed invasive amplifying feedback above-ground this trajectory is not represented below-ground, and restoration legacies dominated 10 years after practices were applied. Restoration practices that limit invasive plant feedbacks and account for soil legacy recovery, therefore offer the best solution for disturbed ephemeral ecosystems.