Holobionts are complex communities comprising a host and its diverse microbiota. Their intricate relationships are crucial for biological processes like nutrient uptake, immune function, and environmental adaptation. However, understanding these complex interactions remains challenging. We review how synthetic biology can help address these challenges. We highlight advances in bacterial biosensor design, engineering interkingdom communication, surface display, and clustered regularly interspaced short palindromic repeats (CRISPR) systems to both understand and manipulate holobiont interactions. We also highlight progress in engineering non-model microbiota members and provide rationale for a new field at the intersection of holobiont research and synthetic biology, which we term de novo holobiont design. The integration of synthetic biology with holobiont research promises to deepen our understanding of host–microbiota relationships and open new frontiers in biotechnology.