The ex-Blues player of the season has taken on the role with the League Two strugglers until the end of the campaign following Wayne Brown’s exit.
Mullins has been at the Colchester Community Stadium since last September, when he arrived from Watford as Steve Ball’s assistant.
Ball departed in February and was replaced by Brown, who lasted just five weeks in the position.
Mullins made 129 appearances for Pompey, scoring three goals, between 2009 and 2012 and also turned out for the likes of Crystal Palace, West Ham and Birmingham in his playing career.
Colchester currently sit in 21st place in League Two - four points above the relegation places.
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