Using the 18S V1-V2 region marker data, we show that a homogenizer protocol during DNA extraction can significantly improve sediment metabarcoding results in terms of captured diversity and inter-replicate homogeneity compared to vortexing only. Pre-PCR pooling of DNA extraction replicates increased observed rarefied richness compared to data from single extracts only, but not to the extent of sample extract replicates amplified individually before pooling. Our results demonstrate that extraction replicates of smaller sediment volumes, in combination with homogenizer treatment and pre-PCR pooling, is a cost-effective way to increase the amount of organism diversity that is recovered from sediment eDNA metabarcoding samples.