Innovative and creative solutions are needed to reduce the substantial carbon footprint of the concrete industry using low-carbon materials. Biochar has been recognised as an environmentally efficient material for concrete production. Also, it is required to build interpretable predictive models to advance modelling-based mix design optimisation. This study uses biochar as a cement substitute in concrete and assesses the mechanical strength using lab tests followed by predictive modelling approaches. Two types of biochar derived from olive pits and wood were used in 2.5 and 5 wt.% of cement. Cubes, cylinders, and beams were cast to test biochar concrete’s compressive, tensile, and flexural strength. The test data were used to develop and validate prediction models for the compressive strength (CS) using linear regression and gene expression programming (GEP) techniques. Moreover, SHapley Additive exPlanation (SHAP) analysis was performed to evaluate the influence of parameters on the CS. The results showed that olive pit biochar was more effective in enhancing the concrete strength than wood biochar due to the reduced particle size. The optimal replacement levels for olive pit biochar were 2.5 wt.% for the CS and 5 wt.% for the split tensile and flexural strength. The GEP model effectively captured the non-linear behaviour of biochar concrete and was more accurate than the linear regression model for the CS. The approach adopted in this study can be used to optimise mix design formulations for biochar concrete. These findings highlight the potential of biochar as a sustainable and effective cement substitute, contributing to the development of greener concrete with improved mechanical performance. Integrating biochar into concrete production can significantly lower the industry’s carbon footprint, promoting environmentally responsible construction practices while maintaining structural integrity.