Filamentous bacteria pose unique challenges for testing multiple variables or growth parameters limiting the use of high-throughput methods. A semi-high-throughput growth assay system was developed to overcome these obstacles and validated for the filamentous actinobacteria Frankia. The 24-well plate assay was versatile for testing multiple growth medium parameters and provided reproducible results across wells and between plates. Under conditions of increased complexity, statistical analysis demonstrated that the variance was dependent on the experimental parameters and not the assay system. The 24-well plate assay was shown to be multipurpose for testing numerous variables on cell growth or other biological properties.