The National Trust Australia (Vic) has deemed both the formal gardens and the buildings of the Abbotsford Convent to be of national heritage significance due to their historic landscape and architectural values. Both are recorded on the Register of the National Estate and the Victorian Heritage Register. When the Abbotsford Convent Foundation took possession of the precinct in 2004, the gardens were totally overgrown with weeds and blackberries. A team of dedicated volunteers and a Green Corp program helped to transform the gardens, which date back to 1902.
The most structured part of the garden is the heritage-listed formal garden, dating from around 1902. The garden still retains elements from an even earlier Abbotsford House garden, including two oaks – Quercus ilex (Holm Oak) and Quercus robur (English Oak). The garden structure has survived almost intact with the rotunda, rock edging to the beds, many fine old trees and encircling edges still evident. Volunteers are now helping to restore the garden as it would have been around 1963.
The design of the formal garden is reminiscent of the naturalistic style popular at the time in England and Australia and seen in Guilfoyle's layout of the Royal Botanic Gardens in Melbourne. The perimeter path provides a series of controlled views and surprise vistas. Early photographs show the presence of many upright conifers such as the Italian Cypress as well as a large number of Radiata Pine, Chinese Fan Pines and Canary Island Palms. There are a number of trees of cultural significance, including a Silky Oak, a Common Alder, a White Poplar and a Honey Locust.
An English Oak is thought to have been planted by Edward Curr, known as 'The Father of Separation', as early as 1850 in the garden of the original St Heliers House. This tree could be regarded as Victoria's Separation Tree and is included on the National Trust's Register of Significant Trees. In a protected environment, it has retained its natural form of low sweeping branches. The area south of the Convent, down to the Yarra River (Birrarung), was originally used by the Sisters as extensive market gardens and vegetable plots.