Quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) are applied for quantifying molecular targets in disease diagnostics, pathogen detection, and ecological monitoring. Uptake of dPCR is increasing due to its higher quantification accuracy relative to qPCR, which stems from its independence from standard curves and its increased resistance to PCR inhibitors. Throughput can be increased through multiplexing, which allows simultaneous quantification of multiple targets. However, multiplexing with dPCR faces unique challenges relative to qPCR. Here, we describe the three-phase development process of non-competing multiplex dPCR assays using target-specific fluorescently labeled hydrolysis probes. We highlight common challenges encountered, along with recommended solutions. Phase 1: In silico assay design; target-specific primers and probes are selected or designed, potential issues with primer and probe interactions are identified, and fluorophores and quenchers are chosen based on dPCR instrumentation. Phase 2: Wet-lab validation; assays are benchmarked using positive controls. Insufficient performance leads to assay redesign, as needed. Phase 3: Assay implementation; assay specificity and sensitivity are validated on relevant sample matrices. Finally, we provide recommendations on the future design and standardization of multiplexed dPCR assays, highlighting the need for better in silico predictions of assay performance, standardizing positive controls, and automating partition classification systems.