Microbiome engineering is a fast-evolving area with relevance for human health, agriculture, and climate management solutions. Despite significant efforts in engineering microbiomes to repair dysbiotic communities, new microbes often fail to establish and/or alter ecosystem function. To identify bacterial and fungal genera with the desired ability to stably incorporate in diverse microbial communities, we retrieved paired 16S and ITS rRNA amplicon sequence data from 1,580 host, soil, and aquatic samples and explored the ecological patterns of the 2,977 bacteria and 1,740 fungal genera detected across all samples. Through this large-scale analysis, we revealed that a small number of bacterial and fungal generalists with high prevalence across all environments positively contribute to the taxonomic diversity of their respective kingdom and explain a large percentage of the variation in the cross-kingdom community structure. We also observed that bacterial and fungal generalists have a significantly higher abundance compared to specialists, or genera whose prevalence was strongly associated with a single habitat - possibly due to their ability to stimulate positive associations with other highly prevalent genera. These findings can streamline existing strategies to identify bacterial and fungal inoculants with a higher probability to establish in recipient ecosystems and confer noticeable changes in their structure and function.