To explore the direction of inter-scale transfer of scalar variance between subgrid scale (SGS) and resolved scalar fields, direct numerical simulation data obtained earlier from two complex-chemistry lean hydrogen–air flames are analysed by applying Helmholtz–Hodge decomposition (HHD) to the simulated velocity fields. Computed results show backscatter of scalar (combustion progress variable $c$) variance, i.e. its transfer from SGS to resolved scales, even in a highly turbulent flame characterized by a unity-order Damköhler number and a ratio of Kolmogorov length scale to thermal laminar flame thickness as low as 0.05. Analysis of scalar fluxes associated with the solenoidal and potential velocity fields yielded by HHD shows that the documented backscatter stems primarily from the potential velocity perturbations generated due to dilatation in instantaneous local flames, with the backscatter being substantially promoted by a close alignment of the spatial gradient of mean scalar progress variable and the potential-velocity contribution to the local SGS scalar flux. The alignment is associated with the fact that combustion-induced thermal expansion increases local velocity in the direction of $\boldsymbol {\nabla } c$. These results call for development of SGS models capable of predicting backscatter of scalar variance in turbulent flames in large eddy simulations.