Bioactive peptides are used in diagnostics and as therapeutic agents in a variety of diseases, as well as inhibitors of bacterial growth in food industry. Recent technological advances in delivery and formulation tools have resuscitated the field of peptide therapeutics, resulting in approx. 60 approved peptide drugs and an annual predicted growth rate of the market of approximately 10%. Whilst the majority of peptides are currently produced by chemical synthesis, recombinant peptide production will become more important in the near future and will play a key role in the competition landscape of peptide therapeutics companies. In particular, this is the case for long and complex peptides containing natural amino acids. Although development of a biotechnological process for recombinant production can be time consuming, larger quantities of peptide can be produced and the environmental impact of the generated waste is lower compared to chemical synthesis. However, recombinant peptide expression must overcome several obstacles in order to be cost-effective and competitive with chemical synthesis. The present review focuses on recombinant peptide production in microbial expression platforms, in particular the expression hosts Escherichia coli and yeast and their respective vectors. Strategies which have been successful in solving drawbacks such as degradation of peptides by cellular proteases, solubility and purification issues, toxicity of recombinant peptides for the producer cells and the introduction of posttranslational modifications are described.