Organoids are stem cell-derived 3D mimetics of tissues and organs, representing an invaluable tool for modelling tissue homeostasis and disease biology, holding great potential for drug development and clinical applications. However, organoid formation relies on the self-organisation of stem cells which offers little control over their architecture, limiting the faithful recapitulation of tissue morphology, experimental accessibility and functionality. Bioengineering approaches have driven the development of organoid-derived on-chip in vitro models addressing current limitations. Here, I engineered innovative "intestine-on-chip" models, termed "mini-intestines", with unprecedented architectural detail and functionality through scaffold-guided organogenesis. First, I examined intestinal lipid metabolism in mini-intestines, assessing the accumulation of lipid droplets (LDs) and validating the findings in vivo. An automated single-cell image quantification pipeline was developed and applied, showing significantly more LDs in Paneth cells (PCs) compared to proliferative intestinal stem cells (ISCs). This suggests that PCs support ISCs by protecting them from lipotoxicity. Moreover, mini-intestines contributed to understanding an in vivo knockout phenotype by demonstrating that LD packaging was impaired in transgenic in vitro tissues. Thus, mini-intestines enabled new insights into intestinal lipid metabolism. Intestinal organoids and bioengineered models successfully mimicked crypt development and intestinal cell type diversity but, so far, lacked an accurate representation of the villus. I developed intestinal epithelia with defined villus compartments in vitro, so-called "bioengineered villi". The hydrogel scaffold was modified to provide villus structures, the culture protocol was adapted, and the resulting bioengineered villi were examined using single-cell transcriptomics and spatial proteomics. The bioengineered villi exhibited accurate enterocyte zonation, including functionally mature villus tip enterocytes, rarely found in conventional organoids. In conclusion, we bioengineered a morphologically and functionally accurate crypt-villus axis in vitro. Secondary lymphoid organs such as lymph nodes spatiotemporally coordinate diverse immune processes relevant to clinical disorders, including inflammatory diseases, cancer, and infections. Faithfully replicating these processes in vitro requires an accurate tissue morphology, which is a major challenge in conventional organoids. Building on my expertise in bioengineering, I developed an on-chip lymphoid model with precise compartmentalisation of immune cells in 3D. Adapting the hydrogel scaffold provided precise control over cell type-specific positioning, enabling stable long-term coculture of lymphatic endothelial, stromal, and immune cells in an organomimetic manner. This model provides unprecedented spatial control, making it the most accurate in vitro lymphoid model to date, with strong potential for studying human adaptive immunity in vitro. In summary, I show that scaffold-guided organogenesis enables i) unique experimental designs, ii) faithful recapitulation of in vivo tissue architecture and function, and iii) modular integration of multi-tissue co-cultures for physiologically relevant studies. This work holds great promise for both fundamental research and translational applications, including drug development and regenerative medicine.