  In recent years, a persistent tension between phenomenological and lattice
QCD determinations of the pion-nucleon $\sigma$-term $\sigma_{\pi N}$ has
developed. In particular, lattice-QCD calculations have matured to the point
that isospin-violating effects need to be included. Here, we point out that the
standard conventions adopted in both fields are incompatible, with the
data-driven extraction based on the charged-pion mass, but lattice-QCD
conventions relying on the mass of the neutral pion to define the isospin
limit. The corresponding correction amounts to $\Delta \sigma_{\pi
N}=3.1(5)\,\text{MeV}$ when evaluated in chiral perturbation theory with
low-energy constants determined from a Roy-Steiner analysis of pion-nucleon
scattering as well as $\sigma_{\pi N}$ itself. It reduces the tension with
lattice QCD, and should be included in the comparison to phenomenological
determinations. We also update the extraction from pionic atoms accounting for
the latest measurement of the width of pionic hydrogen, $\sigma_{\pi
N}=59.0(3.5)\,\text{MeV}$, and provide the corresponding set of scalar
couplings of the nucleon.
