Biological cell factories are capable of producing a wide range of products and support environmentally friendly industrial processes. Currently, the development of new cell factories is time consuming and laborious. It is difficult to efficiently test different combinations of biological parts to identify those for optimal product production. We address this issue by developing an end-to-end platform for engineering Pichia pastoris cells with a focus on enhanced protein expression and secretion. A toolkit of standardised parts was developed to construct large libraries of designs, and an encapsulation technique was evaluated to simplify their analysis.