<p>Microbiome engineering seeks to reshape microbial communities to improve ecosystem function. However, many efforts fail due to inadequate design principles, often resulting in a loss of key microorganisms and disruption of links between the engineered community and its intended function. In contrast, decades of research in macroecology have uncovered key principles governing the relationship between biodiversity and ecosystem function. Here we translate these ecological principles to microbiome engineering, focusing on three stages: microbiome design, colonization and maintenance. We propose new approaches that leverage underlying ecological dynamics—particularly niche dynamics—to optimize diversity and abundance to promote stability and functionality, especially in host-associated microbiomes. We also highlight key research priorities to apply macro-ecosystem insights to microbial systems. Improving microbiome engineering in this way holds promise for solving pressing challenges in medicine and agriculture, while providing understanding of ecological processes that maintain biodiversity across biological scales.</p>