Peter Crane was elected to the Royal Society – the UK academy of sciences in 1998 and was knighted in the UK for services to horticulture and conservation in 2004. He is a Fellow of the American Academy of Arts and Sciences, Foreign Associate of the US National Academy of Sciences, a Foreign Member of the Royal Swedish Academy of Sciences, and a Member of the German Academy Leopoldina. He is the recipient of several honorary degrees from universities in the UK and US, including honorary doctorates of science including from the University of Connecticut in the US and Cambridge University in the UK. He received the International Prize for Biology in December 2014.

Peter Crane has devoted significant time to serving on the Boards of non-profit organizations. He currently serves on the Boards of the Field Museum and Yale-NUS College, and chairs the Board of the Crop Trust.