On board measurement of non-volatile particle number (PN) emissions with portable emissions measurement systems (PEMS) was introduced for the type approval of passenger cars in Europe since 2017 and is foreseen for heavy-duty (HD) vehicles in 2021. First studies on performance of PN-PEMS with HD engine exhaust revealed larger differences between established PN-PEMS techniques than what was observed for passenger cars. Particles forming in selective catalytic reduction (SCR) systems for NOx of late technology HD engines have recently been identified as a potential reason for the observed differences. The formed particles have a size distribution peaking below the regulatory limit of 23 nm and most importantly acquire high (more than one) positive charges at the elevated exhaust temperatures. Precise measurement of such highly charged nanosized particles with PN-PEMS instrumentation utilizing diffusion charger (DC) based counters requires proper conditioning of these charges. Two approaches were investigated in this study: a) an electrofilter (EF) to completely remove charged particles below the regulated size and b) a tandem negative-positive corona (TC) charger to directly condition pre-charged particles. The two technical solutions were tested alongside the unmodified DC-based PN-PEMS, a PN-PEMS utilizing a condensation particle counter (CPC) and a reference stationary PN system using exhaust of two SCR-equipped HD engines. The results confirmed that the particles forming in such SCR systems are responsible for the observed inconsistencies and that both technical solutions efficiently address the interferences of these pre-charged nanoparticles.