This study investigated whether male runners improve running performance, running economy, ankle plantar flexor strength, and alter running biomechanics and lower limb bone mineral density when gradually transitioning to using minimalist shoes for 100% of weekly running. The study was a planned follow-up of runners (n = 50) who transitioned to minimalist or conventional shoes for 35% of weekly structured training in a previous 6-week randomised controlled trial. In that trial, running performance and economy improved more with minimalist shoes than conventional shoes. Runners in each group were instructed to continue running in their allocated shoe during their own preferred training programme for a further 20 weeks while increasing allocated shoe use to 100% of weekly training. At the 20-week follow-up, minimalist shoes did not affect performance (effect size: 0.19; p = 0.218), running economy (effect size: ≤ 0.24; p ≥ 0.388), stride rate or length (effect size: ≤ 0.12; p ≥ 0.550), foot strike (effect size: ≤ 0.25; p ≥ 0.366), or bone mineral density (effect size: ≤ 0.40; p ≥ 0.319). Minimalist shoes increased plantar flexor strength more than conventional shoes when runners trained with greater mean weekly training distances (shoe*distance interaction: p = 0.036). After greater improvements with minimalist shoes during the initial six weeks of a structured training programme, increasing minimalist shoe use from 35% to 100% over 20 weeks, when runners use their own preferred training programme, did not further improve performance, running economy or alter running biomechanics and lower limb bone mineral density. Minimalist shoes improved plantar flexor strength more than conventional shoes in runners with greater weekly training distances.