The EMC3‐Eirene code is improved in many aspects. Ad hoc boundary conditions for intrinsic impurities at the SOL‐core interface are removed by implicitly coupling to a 1D core model. Non‐uniform cross‐field transport coefficients are allowed in the new code version. A particle splitting technique is implemented for improving the Monte Carlo statistic in low‐temperature ranges of most interest. Domain splitting, which was possible for the toroidal direction only, is now feasible for all three directions, facilitating mesh optimization for any specific divertor configuration. Stellarator‐specific constraints on mesh construction have been relaxed. Axisymmetric neutral‐facing components have been moved to cylindrical coordinates. All these features have improved the code performance and capability significantly. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)