We investigate the sensitivity of IceCube(-Gen2) to a scalar leptoquarkscenario with couplings only to heavy quark flavors which may be connected tosolving discrepancies in $B$-meson semileptonic decays. We take into account,for the first time, the non-negligible neutrino-gluon cross section induced byleptoquarks, and we systematically account for indirect and direct constraintswhich have been overlooked in previous studies. We conclude that IceCube(-Gen2)can only probe the light LQ regime, already disfavored by the combination offlavor physics constraints, electroweak precision data and the direct searchesat the LHC.