Hexanoic acid (HA) produced by microorganisms in waterlogged soils causes a decline in plant root O2 consumption, but it is unknown if lack of respiration is due to mitochondrial dysfunction or substrate starvation. We treated Pisum sativum L. roots with 20 mM HA acid at pH 5 and 6 for 1 h and measured leakage of electrolytes, malate, citrate and non-structural carbohydrates (NSC). Afterwards, mitochondria were isolated to assess their functionality, evaluated as electrical potential formation and O2 consumption. HA treatment resulted in root tissue extrusion of K+, malate, citrate and NSC, but the leakage of the organic acids and NSC was increased at pH 5 with the inhibition of O2 consumption and a slight alteration of mitochondrial activity. In conclusion, we propose that undissociated form of HA enters the root cells inducing the efflux of organic acids and NSC and the starvation of mitochondrial respiratory substrates of Krebs cycle with a subsequent decline in O2 consumption.