Studies involving fungal endophytes very often rely on surface-sterilisation of plant samples to enable endophyte isolations. However, surface-sterilisation can be very time-consuming, potentially limiting the number of samples processed. To overcome this limitation, a novel method was developed to bulk surface-sterilise multiple plant tissue samples simultaneously and separately. The method relies on 24 perforated Falcon™ tubes, each containing a sample, sequentially transferred through a series of containers holding the sterilants. The samples that can be surface-sterilised using this method include roots, stems and leaves or entire seedlings. This method increased our throughput by a factor of 24 relative to conventional surface-sterilisation methods.