Areas of karri (Eucalyptus diversicolor F Muell.) regrowth forest subject to timber harvesting (termed ‘coupes’) are thinned two to three times until the forest is predominantly mature, after which it is clearfelled. Forest structure in these karri coupes is characterised by even-aged regeneration that lacks a high degree of structural complexity, such as large mature and senescent trees. The Karri Silvicultural Guideline provides for some stand structural complexity in regenerating karri coupes by stipulating the retention of two immature (secondary) habitat trees per hectare. Mature and senescing (primary) habitat trees are not required by the guideline to be retained within karri clearfell coupes. However, a change in regeneration burning practices away from high intensity, broad-scale regeneration burns to milder, rough-heaped (i.e. piling up of non-commercial vegetation) regeneration burns offers greater scope to protect primary habitat trees if they were to be retained within clearfell coupes. In this study, 298 primary and secondary habitat trees (karri, marri, jarrah and blackbutt) were retained during clearfelling operations. Crown condition and survival of the retained trees were recorded before and 22 months after the regeneration burn. Most retained habitat trees (92%) survived the rough-heaping and regeneration burning. There was a significant decline in the canopy condition of karri (p < 0.001) and marri (p = 0.017) trees to a more intermediate crown senescence; increasing their probability (immediate or longer-term) of hollow occurrence. Assuming that these habitat trees will survive a typical karri harvest rotation (100 years), their presence will enhance the structural complexity of the regenerating stand and provide greater numbers of mature habitat elements, such as tree hollows. Research should continue to assess the survival of the retained habitat trees over a longer time period, and also their use by endemic fauna.