The hemibiotrophic root pathogen Phytophthora medicaginis of chickpea (Cicer arietinum) is an economically important pathosystem where an improved understanding of partial resistance is required to inform resistance breeding. We investigated the molecular pathways controlling resistance responses during the biotrophic, biotrophtic-necrotrophic switch (BNS), and necrotrophic phases of infection by P. medicaginis using parents and progeny from a chickpeaxC. echinospermum backcross that exhibit contrasting Phytophthora root rot resistance. There was a significant separation in the transcriptomic profiles of the chickpea genotypes corresponding to their resistance levels at all three phases of disease. A significant portion of these genes were associated to secondary metabolism, leading us to investigate the metabolomic profiles of all genotypes at the corresponding timepoints of infection. By combining untargeted metabolomics with multivariate dimensionality-reduction modelling, we identified 25 root metabolite profiles during the BNS phase that related to host resistance level. We will present our results pertaining to the three most important metabolites associated to disease resistance from this list of candidate markers for resistance, and our characterisation of how chemical alteration to these metabolic signalling pathways impacted disease resistance. This study demonstrates that markers of disease resistance introduced through introgression can be identified and traced within a population of chickpea, and how understanding the modes of action of these metabolite markers could be used to advance our understanding of hemibiotrphic diseases as well as streamline current disease resistance breeding practices.