Biochar is thought to have great potential as a supplemental amendment in nursery growing media. The knowledge of how to optimize the use of biochar in the nursery setting during the most vulnerable pre-emergence and early seedling stages of the plant, however, is underdeveloped. The current study involves pre-emergence trials in the Pythium aphanidermatum-cucumber pathosystem using a commercial nursery potting mixture amended with up to 3% w:w wood-derived biochar. The major questions were: (i) is pre-conditioning required to elicit suppression of pre-emergence damping-off disease in the Pythium-cucumber system; (ii) what are the changes in bacterial community composition and diversity due to pre-conditioning of the biochar-amended potting medium; and (iii) can the pre-conditioning stage be shortened from 45 days and still provide disease suppression. Pre-conditioning, consisting of pre-planting fertigation of the nursery medium, was found to be needed to achieve suppression of damping-off disease by biochar, with a reduction in pre-emergence damping-off caused by P. aphanidermatum by up to 71%. Illumina sequencing of 16s bacterial gene revealed a significant enrichment in the abundance of bacteria in general and potentially beneficial microorganisms in particular, as well as shifts in microbial community structure as a result of biochar addition. These changes may play an important role in the overall effects of biochar on disease suppression in young seedlings. A pre-conditioning period of only 14 days was found to be effective for disease suppression, which can substantially improve its practical utility for nurseries. © 2019 Elsevier Ltd