Spooner succeeded Jim Gannon in February and helped guide the club to safety with five wins in his first eight games in charge.
After initially joining until the end of the season, alongside Gavin McCann and coach Martin Coyne, the appointment has now been confirmed for 2022/23.
He said: "I am honoured to have been given the opportunity to carry on next season and I am looking forward and excited for what next season brings.
“I would like to thank everyone associated with the Club who have supported me from day one and a special mention to the fans, whose support has been tremendous and helped us survive in this division.”
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