Non-linear effects in the early Universe generate non-zero bispectra of the cosmic microwave background (CMB) temperature and polarization, even in the absence of primordial non-Gaussianity. In this paper, we compute the contributions from isocurvature modes to the CMB bispectra using a modified version of the second-order Boltzmann solver SONG. We investigate the ability of current and future CMB experiments to constrain these modes with observations of the bispectrum. Our results show that the enhancement due to single isocurvature modes mixed with the adiabatic mode is negligible for the parameter ranges currently allowed by the most recent Planck results. However, we find that a large compensated isocurvature mode can produce a detectable bispectrum when its correlation with the adiabatic mode is appreciable. The non-observation of this contribution in searches for the lensing bispectrum from Planck allows us to place a new constraint on the relative amplitude of the correlated part of the compensated isocurvature mode of $f_{rm CIP}=1pm100$. We compute forecasts for future observations by COrE, SO, CMB-S4 and an ideal experiment and conclude that a dedicated search for the bispectrum from compensated modes could rule out a number of scenarios realised in the curvaton model. In addition, the CMB-S4 experiment could detect the most extreme of those scenarios ($f_{rm CIP}=16.5$) at 2 to 3-$sigma$ significance.
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