The deal will keep the 37-year-old at Silver Jubilee Park until the summer of 2024.
This season has been a battle against relegation for the majority of the season and in the end, the Greens only finished a point above North London rivals Harrow Borough in 18th.
Allinson was appointed in November 2019 following a successful spell at Biggleswade Town, who he left having guided them into the play-off picture in the Southern League Premier Division Central.
He had previously enjoyed playing spells with the Waders, Arlesey Town, Stotfold and, most notably, Boreham Wood before a spell as assistant manager at St Albans City under his father, the former Arsenal player Ian Allinson.
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