Engineering clinically relevant cells in vitro holds promise for regenerative medicine, but most protocols fail to faithfully recapitulate target cell properties. To address this, we developed CellNet, a network biology platform that determines whether engineered cells are equivalent to their target tissues, diagnoses aberrant gene regulatory networks, and prioritizes candidate transcriptional regulators to enhance engineered conversions. Using CellNet, we improved B cell to macrophage conversion, transcriptionally and functionally, by knocking down predicted B cell regulators. Analyzing conversion of fibroblasts to induced hepatocytes (iHeps), CellNet revealed an unexpected intestinal program regulated by the master regulator Cdx2. We observed long-term functional engraftment of mouse colon by iHeps, thereby establishing their broader potential as endoderm progenitors and demonstrating direct conversion of fibroblasts into intestinal epithelium. Our studies illustrate how CellNet can be employed to improve direct conversion and to uncover unappreciated properties of engineered cells. Display omitted •The CellNet network biology platform evaluates cell-fate engineering strategies•CellNet reveals incomplete conversion of engineered macrophages and hepatocytes•Conversion to induced hepatocytes specifies intestinal fate, regulated by Cdx2•Induced hepatocytes are endoderm progenitors that can functionally engraft colon A network biology platform, CellNet, enables a more accurate assessment of the fidelity of cellular engineering (e.g., directed differentiation and directed conversion) and provides strategies for improving cell derivations.