New Zealand kauri (Agathis australis) trees are culturally, socially and ecologically significant within northern New Zealand's nutrient‐poor podocarp forest ecosystems. Phytophthora agathidicida is an aggressive oomycete pathogen, capable of killing A. australis across its ecological range, causing the disease known as kauri dieback. The pathogen, like many other forest Phytophthora species, commences as a fine root rot which progresses to collar rot and resinous cankers on the lower trunk. In this study, we investigated the eco‐physiological and fine root responses of kauri to infection by P. agathidicida and tested whether the foliar application of micronutrients (manganese and zinc combined, iron alone, or a trace element mix) affects dieback disease expression. Fortnightly assessments of chlorophyll‐a‐fluorescence were conducted over 12 weeks, and fine root length and tip numbers were recorded at the end of the experiment. None of the micronutrient treatments had a significant physiological effect regardless of pathogen infection. However, contrary to expectations, pathogen infection caused a significant upregulation in photosynthetic activity over time, as the electron transport rate of infected plants was approximately 26% higher than that of control plants at the end of the trial. These results indicate that an increase in the strength of the below‐ground carbon sink through pathogen consumption of labile carbohydrates (sugars), together with pathogen‐induced root damage, triggered upregulation of photosynthesis in the seedlings. Understanding how P. agathidicida infection affects the physiology and resource allocation in kauri is critical to determining the disease aetiology and management options.