However the overwhelming success on the pitch was overshadowed by little visible progress being made in the building of the stadium at James Whatman Way. Before the 2007–08 season had even begun Alan Walker was involved in a freak accident at a coaching course in Belfast which left him temporarily paralysed. Walker made a valiant recovery however, and was back walking and in management by the start of the league season. Maidstone struggled in the new surroundings of the Isthmian League Premier Division and spent the majority of the season near the foot of the table, despite having the services of Chris Smalling at their disposal, however they avoided relegation after beating Folkestone Invicta 1–0 on the last day of the season, a result that relegated Invicta in Maidstone’s place.  In other news 25% of the club was sold to businessman Oliver Ash in February 2008.

The 2008–09 was another tough season for Maidstone. The squad who came so close to relegation the year before was largely dismantled with a whole raft of new players replacing them. During the close season it had become increasingly apparent the club could not afford to field a competitive Isthmian Premier team and fund the building of a new stadium, so with what limited funds the club had seemingly tied up in paying new players it was decided to try and fund the construction at James Whatman Way by bidding for a £1.2million grant from the Football Foundation. The bid was turned down in October 2008 and the club was subsequently put up for sale by chairman Paul Bowden-Brown. However no takeover was forthcoming and as a result of this the club had no choice but to halve their wage bill from £6000 to £3000 per week. The majority of the players took pay cuts and led Maidstone to their best league finish since reforming, finishing a comfortable 15th in the Isthmian Premier table and reaching the 4th qualifying round of the FA Cup.

During the 2009 close season Maidstone moved from their temporary Bourne Park home in Sittingbourne to Ashford Town’s stadium, The Homelands, citing lower rent and a deal to receive a percentage of refreshment takings as the reason for the move. However the move only increased Maidstone’s financial woes due to a sharp drop in attendances, and in December 2009 it was revealed two months of staff pay was to be deferred to the end of the season, a move that led to Alan Walker and Lloyd Hume resigning as managers of the club. Reserve team boss Pete Nott stepped up to the first team managers role and led Maidstone to an 18th-place finish, avoiding relegation with a game to spare.

In October 2010 the club was taken over by shareholder Oliver Ash and Terry Casey with Paul Bowden-Brown stepping down as chairman. In November 2010 the club’s new directors sacked first team boss Peter Nott and his backroom staff with the team bottom of the table and out of the FA Cup. Former Gravesend & Northfleet manager Andy Ford was swiftly appointed manager, but he could not improve the club’s fortunes and resigned in March 2011 with the club bottom of the league and 8 points adrift from safety. Club captain Jay Saunders was appointed caretaker manager until the end of the season, and although he oversaw the team to 5 wins from nine games he could not save Maidstone from relegation. Saunders was subsequently given the permanent managers job.

In the 2011 close season the club returned to groundshare at Sittingbourne’s Bourne Park after their two-year spell at Ashford’s Homelands Stadium, and soon after construction finally began on the club’s new ground The Gallagher Stadium. The club finished the season in sixth place, just outside the play-offs. The 2012 close season saw Maidstone finally come home, moving into the Gallagher Stadium in July 2012. The club opened the £2.6 million stadium with a showpiece friendly against Brighton & Hove Albion in front of a sell-out crowd. After a two-horse race for the Isthmian League Division One South title with Dulwich Hamlet, and regularly playing in front of crowds of 1,500+, Maidstone eventually won promotion to the Isthmian League Premier Division after beating Faversham Town 3–0 in the Isthmian League Division One South play-off final.

During the 2014–15 season, Maidstone United qualified for the first round proper of the FA Cup for the first time in their history. Maidstone played a goalless draw away to Stevenage of League Two and in the replay at home in front of a capacity crowd went through to the second round proper, winning 2–1. In the second round Maidstone lost 3–1 at Wrexham of the Conference Premier. Maidstone United went on to win the Isthmian Premier title following a season-long battle with Margate, then Dulwich Hamlet and finally Hendon. The title was effectively won at Champion Hill, home of Dulwich Hamlet, on 18 April 2015 with Maidstone United drawing 0–0 and Hendon drawing 0–0 away at Grays Athletic. The near-1,000 travelling Stones fans celebrated on the pitch with the Dulwich Hamlet fans, their best position since reforming. The title was officially won on home soil on 25 April 2015 with a 3–2 win over East Thurrock United.