A clean interface between two Weyl semimetals features a universal, field-linear tunnel magnetoconductance of (𝑒2/ℎ)𝑁ho per magnetic flux quantum, where 𝑁ho is the number of chirality-preserving topological interface Fermi arcs. In this work we show that the linearity of the magnetoconductance is robust with respect to interface disorder. The slope of the magnetoconductance changes at a characteristic field strength 𝐵arc—the field strength for which the time taken to traverse the Fermi arc due to the Lorentz force is equal to the mean inter-arc scattering time. For fields much larger than 𝐵arc, the magnetoconductance is unaffected by disorder. For fields much smaller than 𝐵arc, the slope is no longer determined by 𝑁ho but by the simple fraction 𝑁L𝑁R/(𝑁L+𝑁R), where 𝑁L and 𝑁R are the numbers of Weyl-node pairs in the left and right Weyl semimetal, respectively. We also consider the effect of spatially correlated disorder potentials, where we find that 𝐵arc decreases exponentially with increasing correlation length. Our results provide a possible explanation for the recently observed robustness of the negative linear magnetoresistance in grained Weyl semimetals.