| Champions League Qual. | M. | W | D | L | goals | |||
| at home | 1 | 0 | 0 | 1 | 1 | : | 4 | |
| Away | 1 | 0 | 0 | 1 | 0 | : | 6 | |
| ∑ | 2 | 0 | 0 | 2 | 1 | : | 10 | |
| Europa Conference League | M. | W | D | L | goals | |||
| at home | 1 | 1 | 0 | 0 | 1 | : | 0 | |
| Away | 1 | 0 | 0 | 1 | 0 | : | 2 | |
| ∑ | 2 | 1 | 0 | 1 | 1 | : | 2 | |
| overall | M. | W | D | L | goals | |||
| at home | 2 | 1 | 0 | 1 | 2 | : | 4 | |
| Away | 2 | 0 | 0 | 2 | 0 | : | 8 | |
| Neutral Place | 0 | 0 | 0 | 0 | 0 | : | 0 | |
| ∑ | 4 | 1 | 0 | 3 | 2 | : | 12 | |
| Champions League Qual. | |||||
| 1999/2000 | 1. Round | FC Flora | - | Partizan | 1:4 (0:2) |
| 1999/2000 | 1. Round | Partizan | - | FC Flora | 6:0 (3:0) |
| Europa Conference League | |||||
| 2021/2022 | Group B | FC Flora | - | Partizan | 1:0 (1:0) |
| 2021/2022 | Group B | Partizan | - | FC Flora | 2:0 (2:0) |
|
For games that were decided on penalties the score after 120 minutes will be included in the ranking |
Estonia 
![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}
