In 2021 Macfarlane was elected as a Fellow of the Royal Society Te Apārangi. Her nomination said "Sonja has played a key role in the advancement of alternative ways for educators and psychologists to improve cultural awareness and responsivity, leading to the implementation of practices that accrue benefits for Māori learners and clients. Her culturally-grounded publications and applied practice models in these disciplines have established her as an authority on the ways professionals can engage authentically within their professional spaces." Also in 2021, Macfarlane was awarded the Dame Marie ClayAward by the New Zealand [Psychological Society].