Abstract: In dark-matter annihilation channels to hadronic final states, stable particles – such as positrons, photons, antiprotons, and antineutrinos – are produced via complex sequences of phenomena including QED/QCD radiation, hadronisation, and hadron decays. These processes are normally modelled by Monte Carlo (MC) event generators whose limited accuracy imply intrinsic QCD uncertainties on the predictions for indirect-detection experiments like Fermi-LAT, Pamela, IceCube or Ams-02. In this article, we perform a comprehensive analysis of QCD uncertainties, meaning both perturbative and nonperturbative sources of uncertainty are included – estimated via variations of MC renormalization-scale and fragmentation-function parameters, respectively – in antimatter spectra from dark-matter annihilation, based on parametric variations of the Pythia 8 event generator. After performing several retunings of light-quark fragmentation functions, we define a set of variations that span a conservative estimate of the QCD uncertainties. We estimate the effects on antimatter spectra for various annihilation channels and final-state particle species, and discuss their impact on fitted values for the dark-matter mass and thermally-averaged annihilation cross section. We find dramatic impacts which can go up to O(10%) for the annihilation cross section. We provide the spectra in tabulated form including QCD uncertainties and code snippets to perform fast dark-matter fits, in this github repository.