Organic vegetable growers are interested in using the “soil block” method for transplant production as an alternative to plastic flats. The soil block method compresses growing media into a freestanding block in contrast to the cells of a plastic flat. Anecdotal evidence of soil block–grown transplants with increased vigor and root development exists, but limited research has been conducted to evaluate these claims. Furthermore, identifying commercial growing medium for certified organic transplant production is needed. The objective of this study was to compare growth parameters and root development of cucumber (Cucumis sativus) and pepper (Capsicum annum) transplants grown in soil blocks and plastic flats, in combination with four commercially available certified organic media (Beautiful Land Products “Soil Blocking Mix,” Purple Cow Organics “Seed Starter Mix,” Cowsmo “Green Potting Soil,” and Vermont Compost Company “Fort Vee”). A volume-based 50% peat, 25% compost, 12.5% perlite, and 12.5% vermiculite growing medium was also evaluated. A split-plot randomized complete block design with four replications was used with growing method as the whole plot factor and medium as the subplot factor. ‘Marketmore 76’ cucumbers and ‘Yankee Bell’ peppers were seeded in 50-cell flats and soil blocks made with Johnny’s Selected Seeds Stand-up 12 Soil Blocker. Data were collected on growth parameters by destructively sampling cucumbers 3 weeks after seeding, and peppers 5, 6, and 7 weeks after seeding. Root development was evaluated using WinRHIZOTM at the last sampling. Cucumber and pepper transplants performed differently in soil blocks and flats. Cucumbers grown in flats had a significantly greater dry weight than those grown in soil blocks, by 20% in 2022 and by 38% in 2023. In contrast, pepper transplants grown with the soil block method had between 50% and 130% greater dry weight in the final sampling in 2022. Cucumber and pepper transplants grown with Cowsmo “Green Potting Soil” performed poorly, with an up to 144% lower dry weight and up to 167% lower root surface area than transplants grown with the other media. Root development correlated with shoot development, without a specific advantage in soil blocks, although differences in root system architecture should be investigated. The evaluated Beautiful Land Products, Purple Cow Organics, and Vermont Compost Company media can all be considered suitable for growing certified organic vegetable transplants in both soil blocks and flats. Further research is warranted to better optimize the soil block technique, investigate optimum soil block bulk density, and inform growers of appropriate commercially available certified organic growing media for organic vegetable transplant production.