Axion-like-particles (ALPs) emitted from the core of a magnetar can convert to photons in its magnetosphere. The resulting photon flux is sensitive to the product of $(i)$ the ALP-nucleon coupling $G_{an}$ which controls the production cross section in the core and $(ii)$ the ALP-photon coupling $g_{agamma gamma}$ which controls the conversion in the magnetosphere. We study such emissions in the soft-gamma-ray range (300 keV to 1 MeV), where the ALP spectrum peaks and astrophysical backgrounds from resonant Compton upscattering are expected to be suppressed. Using published quiescent soft-gamma-ray flux upper limits in 5 magnetars obtained with $CGRO$ COMPTEL and $INTEGRAL$ SPI/IBIS/ISGRI, we put limits on the product of the ALP-nucleon and ALP-photon couplings. We also provide a detailed study of the dependence of our results on the magnetar core temperature. We further show projections of our result for future $Fermi$-GBM observations. Our results motivate a program of studying quiescent soft-gamma-ray emission from magnetars with the $Fermi$-GBM.