Transport engineering strategies use altered expression of transporter proteins to change metabolite distribution within an organism. The production of plant specialized metabolites in microbial cell factories encounters a set of challenges that could benefit from the implementation of transport engineering technology. The range of challenges includes premature pathway termination due to secretion of intermediates, feedback inhibition due to inefficient export of final products, low yields in bioconversion processes due to inefficient import of precursors, and poor connectivity between subcellular compartments expressing different parts of complex biosynthetic pathways. We highlight the latest examples of transport engineering in microbial cell factories producing plant specialized metabolites, identify the current knowledge gap, and propose future research for advancing the field.