The development and standardization of an effective inoculation technique are essential for reliable screening of crop genotypes. In this study, three inoculation methods—in vitro paper towel, in vitro agar, and soil inoculation in pots—were tested to evaluate the pathogenic potential of Macrophomina phaseolina, the causative agent of dry root rot (DRR). Since the pathogenicity of M. phaseolina is influenced by environmental factors, identifying a robust inoculation method is critical. Among the three techniques, the paper towel inoculation method resulted in the highest seedling mortality of 66.66% in cluster beans and 86.67% in cowpeas within just ten days, demonstrating its effectiveness. The agar inoculation technique, while successful, required 15 days to confirm pathogenicity, with seedling mortality rates of 63.33% for cowpeas and 53.33% for cluster beans. In contrast, the soil inoculation method showed comparatively lower mortality rates, with 36.66% for cluster beans and 26.67% for cowpeas. Based on these findings, the paper towel method emerged as the most efficient technique for inducing rapid pathogenicity in M. phaseolina in both cowpeas and cluster beans. Its suitability was further validated through the screening of released varieties of these crops compared against the soil inoculation method. Notably, genotypes that appeared moderately resistant under the soil inoculation method were found to range from susceptible to highly susceptible when evaluated using the paper towel technique. These results underscore the reliability of the paper towel method as a rapid and robust screening tool for identifying resistant genotypes of cowpea and cluster bean on a larger scale.