Rising global demand for food and fibre requires more efficient and sustainable fertilizer strategies. Biochar mineral complexes (BMC) are being developed for use as an organic alternative to conventional synthetic fertilizers, or to supplement conventional fertilizers applied at lower rates. Biochar can change electrochemical properties such as zeta potential (ZP) that influence nutrient use efficiency. However, the impact of BMCs on the ZP of plant roots remains unknown. This study investigated the effects of BMC on root zeta potential, nutrient leaching, and yield in an intensive protected cropping system. A novel BMC was developed and tested in four treatments: synthetic fertilizer, organic fertilizer, BMC with half-rate organic fertilizer, and BMC alone. Organic fertilizer significantly increased negative root ZP compared with other treatments, largely due to higher concentrations of –COOH and –OH functional groups on the potting media. Treatments containing organic fertilizer also increased pH and cation exchange capacity (CEC), enhancing nutrient availability and retention relative to synthetic fertilizer. Yield was greatest with synthetic fertilizer; however, BMC combined with half-rate organic fertilizer achieved similar yields to full-rate organic fertilizer. This indicates that BMC co-applied with half-rate organic fertilizer should be considered by farmers to be a viable alternative to full-rate organic fertilizer regimes to reduce net inputs and risk of negative environmental impacts from over-fertilization.