The main objective of this research was to analyze whether selection under conventional conditions (indirect selection) is as effective as selection under organic conditions (direct selection) to develop varieties suitable for organic farming systems. Two F3 barley (Hordeum vulgare L.) populations ‘Primus’/‘Idumeja’ (P/I) and ‘Anni’/‘Dziugiai’ (A/Dz) targeted for organic variety development were selected in two organically and two conventionally managed environments during F3 to F3:6. From there, the performance of the five best F3:6 lines selected in each of the four environments from each cross (in total, 40 lines) were compared at all four sites during two years. For obtaining varieties adapted to organic conditions for the P/I cross, it did not matter at which condition the selection was performed. For A/Dz, the best selection results in terms of yield, combined with other traits included for an organic ideotype, were achieved under well-managed organic conditions. We conclude that direct and indirect selection in early breeding stages are equally suitable for the development of cultivars for organic conditions if (i) care is taken that selection considers not only yield, but also other traits important for organic growing conditions, (ii) selection is not performed under too stressful conditions, and (iii) testing in later stages of the breeding program is conducted under various organic farming conditions for the best recommended varieties for organic agriculture.