Landlord Freshwater submitted a planning application to build the store and refurbish neighbouring flats, Arlington House, in January 2011.
It then appealed to the government in October 2011 on the grounds of non-determination because Thanet District Council had not made a decision on the scheme.
Last week, retail expert Mary Portas wrote to Pickles asking him to block the plans which she described as a "disturbing threat" to the town. Margate is one of 27 "Portas pilot" towns which have shared a £1.2 million government fund to revive their high streets.
A letter sent out by the Planning Inspectorate on behalf of Pickles said the reason for the call in was that "the appeal involves proposals which involve any main town centre use or uses where that use or uses comprise(s) over 9,000 square metres gross floorspace (either as a single proposal or as part of or in combination with other current proposals) and which are proposed on a site in an edge-of-centre or out-of-centre location that is not in accordance with an up-to-date development plan document."
Local campaign group Friends of Arlington Margate (FOAM) called the secretary of state's intervention "unprecedented". In a statement the group said it felt "vindicated" that it had participated in the public inquiry process. "This is a large and far ranging development proposal", it added.