This　study　compared　the　simulation　results　of　the　side-stream　membrane-aerated　biofilm　reactor　(MABR)　in　terms　of　total　nitrogen　(TN)　removal　and　N2O　production　obtained　by　the　conventional　comammox-exclusive　biological　nitrogen　removal　(BNR)　model　and　the　novel　BNR　model　with　comammox-related　model　structures/parameters.　Even　though　the　conventional　comammox-exclusive　MABR　obtained　＞85　%　TN　removal　over　a　wide　range　of　substrate　conditions　and　achieved　up　to　∼92.0　%　TN　removal,　it　suffered　from　0.90　%-4.80　%　N2O　production.　Comparatively,　despite　the　significantly　lower　N2O　production　(0.01　%-0.06　%),　due　to　the　undesired　full　nitrification　of　comammox　bacteria,　the　novel　comammox-inclusive　MABR　failed　to　provide　adequate　nitrite　for　anammox　bacteria　under　exceeding　substrate　conditions　and　only　obtained　the　maximum　∼88.0　%　TN　removal　through　comammox　bacteria-based　partial　nitritation/anammox.　Both　MABRs　should　be　operated　at　a　moderate　hydraulic　retention　time　(e.g.,　4.0　d)　with　a　sufficient　biofilm　thickness　(e.g.,　≥300　μm)　to　attain　efficient　TN　removal　and　reduced　N2O　production.　©　2025　The　Author(s)