Doe is currently in his fifth season with the Daggers, making him the longest-serving member in the club's squad, and has featured in all of their 35 league games to date this term.
His current deal was due to expire at the end of this campaign but he has agreed a new two-year arrangement.
Interim manager Wayne Burnett said: "I am delighted Scott wants to stay and be a part of what we are doing here.
"With him signing the new deal it shows the football club are keen to retain the service of our key players. Scott has had a great season so far and I am looking forward to working with him further."