Callum Roberts marked his 100th appearance for in-form Scunthorpe with the only goal against Southend at the Attis Arena in the National League.
The former Newcastle forward capitalised on a mix-up in the visiting defence to fire into the bottom corner in first-half stoppage time.
Danny Whitehall hit a post for the home side early in the second half as they secured a seventh win from an eight-game unbeaten run in the division.
Andy Dallas, twice, and substitute Charley Kendall went close for Southend, for whom captain Nathan Ralph saw his 200th appearance for the club last just 13 minutes before being forced off with an injury.
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