Gillingham opened the scoring in their pre-season match at Southend with a controversial goal but went on to score twice more.

The linesman on the far side at Roots Hall felt Jack Nolan’s headed effort had crossed the line near the end ot the first half. While debate continued the Gills added a quick second through Jayden Clarke.

Former Gillingham striker Josh Walker got a goal back for Southend before Nolan’s deep cross crept in to re-establish a two-goal advantage.

Gillingham were again without a handful of senior players, missing Ethan Coleman, Armani Little, Jonny Williams, Elliott Nevitt, Josh Andrews and George Lapslie.

Youth players continued to make up the numbers but the starters were given an hour at Southend.

Recent addition Marcus Wyllie started upfront with Aaron Rowe operating in support with Jayden Clarke and Jack Nolan on the flanks.

National League side Southend had created several good openings against the Gills with their right-back Gus Scott-Morris putting two efforts wide of the mark.

Max Clark also headed a dangerous free-kick clear from under his own bar from Oli Coker’s free-kick.

Gillingham appeared to have a slice of fortune for the opener. Only one side of the pitch was filled with fans, and on the opposite side the linesman had his flag raised when a move from the Gills ended with Nolan hitting the woodwork before being cleared.

Instead of a free-kick, however, the referee pointed back to the centre-circle to indicate a goal, much to the surprise of most. Replays later suggested that the ball had indeed crossed the line.

The move had come about after United defender Harry Taylor had been robbed of possession by Rowe, who played in Wyllie who in turn sent McKenzie in and his cross was met by Nolan. His effort went over the line, with Oli Coker clearing from behind the goal line.

A minute later and Clarke - who scored twice in the midweek win over Dartford - was on the scoresheet again, played in on goal and finishing well past goalkeeper Collin Andeng-Ndi.

The match had only just been restarted when Southend got a goal back, scored by former Gills player Josh Walker. Their 26-year-old summer recruit, who scored once in 16 appearances for Gillingham last season, was in the right place to fire the ball home for Southend, slotting home his third goal of pre-season.

Nolan was claiming Gills’ 55th minute goal that made it 3-1 to Bonner’s men. His deep ball into the box found the net, with Wyllie and a defender both attempting to get a touch on the ball.

Southend’s James Morton - who once played a handful of minutes on loan with the Gills - almost put the ball in his own net with a long-range pass back to his goalie, narrowly hitting the ball wide of the post.

Wyllie narrowly missed with a header from Hutton’s cross before the Gills changed their whole outfield team on the hour mark.

Moments after coming on there was concern when Joe Gbode fell over the barriers in front of the Gillingham fans. Medical staff rushed to his aid but he came back on soon enough, nursing a sore shoulder.

The substitutions gave the Gills a young look in the latter stages with Stanley Skipper and Harry Waldock in the centre of midfield. Harry Webster and Sam Gale were the full-backs.

Youth defender Webster picked up a late booking for a trip on one of Southend’s trialists.

Another Southend trialist was denied with a fine save from Jake Turner as the hosts created several opportunities late on. At the other end Harry Bridle went close to adding a fourth for the Gills.

Southend: Andeng-Ndi (Trialist 65mins), Scott-Morriss, Kensdale, Bridge (Trialist 80mins), Cardwell (Wood 65mins), Walker (Ralph 63mins), Gubbins, Taylor (Waldron 63mins), Miley, Morton, Coker (Trialist 65mins). Subs not used: Faulkner, MacDonald, Shobawale.

Gillingham: Turner, Hutton (Webster 63mins), Clark (Gale 63mins), Ehmer (Hawkins 63mins), Ogie (Masterson 63mins), Dieng (Skipper 63mins), McKenzie (Waldock 63mins), Clarke (Nadesan 63mins), Rowe (E Williams 63mins), Nolan (Bridle 63mins), Wyllie (Gbode 63mins). Sub not used: Morris.

Referee: Danial Baines

Attendance: 2,225 (278 away)