Work on the £20million restoration project began in autumn 2019 and is due to be finished by the end of the year, around 12 months later than expected.
The huge tower crane was floated down the river by barge in January 2020 to do the heavy lifting for the development.
City of York Council says the restoration of the Guildhall is set to be complete by the end of 2021 - about a year later than the predicted completion date of autumn 2020.
Work has continued on the site throughout the pandemic, but the programme has been hit by several setbacks including high river levels throughout February 2019, the discovery of historic human remains on the land, further archaeological items and a shortage of some materials as a result of the pandemic.
The six bodies discovered are thought to have been monks buried in the cemetery of an Augustinian priory in the 15th century.The river was used to transport materials to and from the site to avoid construction traffic clogging up narrow city centre streets. Heavy construction work at the site has now finished and the tower crane has been dismantled by a separate 100-tonne crane that is working from a barge on the River Ouse.
When the Guildhall redevelopment project is finished the University of York is set to take a 15-year lease on the venue to create a hub for businesses and events.
The site will also boast a cafe, separate riverside restaurant, offices, meeting rooms and conference space.
The cost of the project has spiralled since initial proposals to refurbish the site were first put forward in 2013 and in 2018 the council pulled out of a £9m deal to transform the site.
Since the start of the refurbishment work in 2019, the costs have increased by at least a further £1.5m.
The Guildhall was the home of City of York Council until 2013, when the local authority moved to West Offices near the Grand Hotel and launched a review of the condition of the historic buildings.
Investigations found it was in need of extensive work to repair structural problems.
The Guildhall, which sits alongside the River Ouse, was originally built in the 15th century. Significant repairs took place to repair the building after a fire during the Second World War, in the Baedeker raids in 1942.
The Guildhall is owned by the council and is made up of Grade I, II* and II listed buildings built around a 15th-century main hall.
Economic experts have forecast that when the redeveloped venue reopens it will create up to 160 jobs, according to the University of York.