The £40 million scheme, in a valley on the eastern outskirts of Truro, was approved by Cornwall Council in March last year despite widespread opposition.
And last month, the final piece of the jigsaw was put in place as planners approved the accompanying 1,350-space park-and-ride scheme to serve the city.
It has now emerged that Truro City Council has applied for a judicial review of the permission granted by Cornwall Council.
Truro City Council clerk Roger Gazzard said: "We have written to the court with our grounds for asking for a judicial review. The court will ask the planning authority to respond to that and then make a decision on whether we have an arguable case or not."
Mr Gazzard said grounds for challenging the decision included that the Waitrose scheme was out of step with the development plan for the city and that Cornwall Council had "misapplied" its own affordable housing policy.
It is also arguing that the permission for the scheme – known as the Truro Eastern District Centre – was "premature" given the absence of Cornwall Council's "local plan" which will set out the shape of future development across the county.
Before Christmas, the city council voted to appoint a legal team to assess the chances of success in trying to block the plans in the courts.
Councillors believe the new supermarket would be detrimental to city traders and that any traffic problems eased by the park and ride scheme would be outweighed by the store.
Mr Gazzard said any decision by the court was likely to take "weeks rather than months".
As Cornwall Council's planning committee last month passed plans for the park and ride scheme, some members took the opportunity to again express that frustrations with the project which includes 97 homes and the promise of about 200 new jobs
Doris Ansari, Lib Dem councillor for Truro, said: "I am sad we are losing one of our most beautiful valleys at the entrance to our city. It's hurt me more than any other planning application over 42 years as a local government representative. It's a sad, sad day for Truro because there was a possibility Waitrose might move into the city centre but they preferred a greenfield site."
A spokesman for Cornwall Council yesterday said it would contest the city council's application. He said: "Cornwall Council will be carefully considering the grounds on which Truro City Council have brought a claim for judicial review in respect of the Truro Eastern District Centre but are confident that the decision to award planning permission is lawful and intend to robustly defend the application."
