[3] Engelhardt worked as a postdoctoral researcher at the University of Chicago in the Department of Human Genetics with Matthew Stephens from 2008 to 2011.

[5] In August 2022, she moved to California, she now holds the position of Professor at Stanford University and Gladstone Institute of Data Science and Biotechnology.

[16] Post tenure, Engelhardt's research in these latent variable models has expanded to include single cell sequencing, with a particular focus on spatial transcriptomics.

Engelhardt has been recognized by several awards including an Alfred P. Sloan Fellowship in Computational Biology,[22] a National Science Foundation CAREER Award,[23] two Chan Zuckerberg Initiative grants for the Human Cell Atlas,[24] and a Fast Grant for her recent work on COVID-19.

[29] Engelhardt served on the Board of Directors (2014–2017) and the Senior Advisory Council (2017–present) for Women in Machine Learning.