| Period | Manager | Country | born |
| 25/11/2024 - 31/12/2025 | Konstantin Vassiljev |
|
16/08/1984 |
| 12/07/2024 - 24/11/2024 | Taavi Viik |
|
30/12/1986 |
| 07/12/2023 - 11/07/2024 | Norbert Hurt |
|
16/04/1983 |
| 31/08/2018 - 31/12/2023 | Jürgen Henn |
|
02/06/1987 |
| 01/07/2018 - 30/08/2018 | Arno Pijpers |
|
21/04/1959 |
| 05/01/2018 - 30/06/2018 | Jürgen Henn |
|
02/06/1987 |
| 02/01/2017 - 31/12/2017 | Arno Pijpers |
|
21/04/1959 |
| 13/07/2016 - 31/12/2016 | Argo Arbeiter |
|
05/12/1973 |
| 08/07/2016 - 13/07/2016 | Jürgen Henn |
|
02/06/1987 |
| 01/01/2014 - 08/07/2016 | Norbert Hurt |
|
16/04/1983 |
| 15/10/2012 - 31/12/2013 | Marko Lelov |
|
21/11/1973 |
| 01/07/2010 - 14/10/2012 | Martin Reim |
|
14/05/1971 |
| 01/07/2009 - 30/06/2010 | Tarmo Rüütli |
|
11/08/1954 |
| 01/01/2006 - 31/12/2008 | Pasi Rautiainen |
|
18/07/1961 |
| 01/10/2004 - 31/12/2005 | Janno Kivisild |
|
05/08/1977 |
| 01/11/2000 - 30/09/2004 | Arno Pijpers |
|
21/04/1959 |
| 01/01/2000 - 31/12/2000 | Tarmo Rüütli |
|
11/08/1954 |
| 01/07/1995 - 31/12/1999 | Teitur Þórðarson |
|
14/01/1952 |
| 01/09/1993 - 30/09/1995 | Roman Ubakivi |
|
24/03/1945 |
| 01/07/1992 - 30/06/1993 | Raimundas Kotovas |
|
![FC Flora [Women]](https://s.hs-data.com/bilder/wappen/mini/30430.gif?fallback=png "FC Flora [Women]"){kind=small}
![FC Flora [Youth]](https://s.hs-data.com/bilder/wappen/mini/24240.gif?fallback=png "FC Flora [Youth]"){kind=small}
