Wambugu is the recipient of IITA's (International Institute of Tropical Agriculture, Nigeria) Award, 1981; KARI’s 1989 Crop Science Award for outstanding scientist of the year; International Potato Center’s (CIP) Regional Research Award/Grant, 1989; Farmers Support Award, Pyrethrum Marketing Board of Kenya, 1990; recognised as an exemplary PhD candidate, Virology Division of Horticultural Research International in England and KARI, 1991; Monsanto Company Outstanding Performance Award, 1992, 1993; first place medal winner, Global Development Network Awards, KARI Year 2000; World Bank Global Development Network Award in 2000 for successful introduction of the tissue-culture banana in Kenya and Woman of the Year by the "Eve Magazine".One of the latest awards is the Yara Prize that Dr. Wambugu received in 2008 from the Norway-based Yara Foundation for her significant contribution to fight hunger and poverty in Africa.