| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | Qualification or relegation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Kelantan United (C, P) | 26 | 21 | 3 | 2 | 93 | 20 | +73 | 66 | Promotion to 2020 Malaysia Premier League |
| 2 | Kuching (O, P) | 26 | 18 | 5 | 3 | 58 | 21 | +37 | 59 | Qualification for Play-offs round[a] |
| 3 | Armed Forces | 26 | 13 | 10 | 3 | 62 | 22 | +40 | 49 | |
| 4 | Puchong Fuerza | 26 | 13 | 6 | 7 | 71 | 40 | +31 | 45 | |
| 5 | Ultimate | 26 | 13 | 6 | 7 | 76 | 48 | +28 | 45 | |
| 6 | Protap | 26 | 11 | 4 | 11 | 47 | 58 | −11 | 37 | |
| 7 | BTK | 26 | 10 | 5 | 11 | 52 | 49 | +3 | 35 | |
| 8 | DDM | 26 | 10 | 4 | 12 | 60 | 54 | +6 | 34 | |
| 9 | SAMB | 26 | 9 | 6 | 11 | 38 | 38 | 0 | 33 | |
| 10 | Batu Dua | 26 | 8 | 3 | 15 | 46 | 72 | −26 | 27 | |
| 11 | Johor Bahru | 26 | 6 | 7 | 13 | 40 | 53 | −13 | 25 | |
| 12 | Langkawi Glory United | 26 | 7 | 4 | 15 | 47 | 63 | −16 | 25 | |
| 13 | Penjara (R) | 26 | 6 | 6 | 14 | 36 | 61 | −25 | 24 | Relegation to Malaysia M4 League |
| 14 | Tun Razak (R) | 26 | 2 | 1 | 23 | 17 | 140 | −123 | 7 |
Updated to match(es) played on 17 November 2019. Source: AFL
Rules for classification: 1) Points; 2) Goal difference; 3) Number of goals scored.
(C) Champions; (O) Play-off winners; (P) Promoted; (R) Relegated
Notes:
Rules for classification: 1) Points; 2) Goal difference; 3) Number of goals scored.
(C) Champions; (O) Play-off winners; (P) Promoted; (R) Relegated
Notes:
- ^ Two teams from runners-up of M3 and last placed team from Premier League play-offs for promotion to the 2020 Malaysia Premier League.