18th-placed Wacker Burghausen were eventually spared from relegation after 5th-placed Kickers Emden voluntarily retracted their application for a license because of financial issues.
FC Kleve (both West), TSV Großbardorf and SpVgg Unterhaching II (both South) were relegated at the end of the 2008–09 season.
Furthermore, FSV Oggersheim (West) and Viktoria Aschaffenburg (South) withdrew from the league due to financial issues.
SC Goslar 08 as winners of a round between the champions of the fifth-level leagues on the territory of the former Oberliga Nord, Tennis Borussia Berlin as NOFV-Oberliga Nord champions and ZFC Meuselwitz as winners of the NOFV-Oberliga Süd joined the Northern division.
Finally, SG Sonnenhof Großaspach as winners of the Oberliga Baden-Württemberg, SpVgg Weiden as Bayernliga champions and FC Bayern Alzenau as Hessenliga runners-up were added to the Southern division; Alzenau were granted promotion because Hessenliga champions SC Waldgirmes were not able to meet the necessary licensing criteria.