Tissue complexity emerges from interactions of components across various biological systems, such as exogenous factors from the microbiota and different host cellular entities. These interactions can be characterized in multiple domains including genetic, spatial, and biochemical. Here we will discuss current tools that enable spatial and transcriptional profiling of individual cells, multiplex microscopy and single-cell RNA-seq, respectively, and their integration to dissect tissue-level complexity. We present several tools to interrogate these data types and demonstrate their applications in characterizing the function of intestinal tuft cells, the sentinel cell type linking the microbiome and the host. These emerging techniques will play a key role in understanding the role of complexity, for example, microbiome-host interactions, in dictating tissue function in homeostasis and dysfunction in human diseases.