Spatial transcriptomics, proteomics, and epigenomics are innovative technologies which offer an unparalleled resolution and wealth of data in understanding and the interpretation of cellular functions and interactions. These techniques allow researchers to investigate gene and protein expressions at an individual cell level, revealing cellular heterogeneity within, for instance, bioengineered tissues and classifying novel and rare cell populations that could be essential for the function of the tissues and in disease processes. It is possible to analyze thousands of cells simultaneously, which gives thorough insights into the transcriptomic view of complex tissues. Spatial transcriptomics combines gene expressions with spatial information, conserving tissue architecture and making the mapping of gene activity across different tissue regions possible. Despite recent advancements in these technologies, they face certain limitations. Single-cell transcriptomics can suffer from technical noise and dropout events, leading to incomplete data. Its applicability has been limited by the complexity of data integration and interpretation, although better resolution and tools for the interpretation of data are developing fast. Spatial proteomics and spatial epigenomics provide data on the distribution of proteins and the gene regulatory aspects in tissues, respectively. The disadvantages of these approaches include rather costly and time-consuming analyses. Nevertheless, combining these techniques promises a more comprehensive understanding of cell function and tissue organization, which can be predicted to be useful in achieving better knowledge of cell guidance in tissue-engineered constructs and a higher quality of tissue technology products.