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Group standing after matches conducted upto 10th November 2016
Group A
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | Goans S. C. | 3 | 3 | 0 | 0 | 20 | 1 | 19 | 9 | |
| 2 | Mumbai United | 3 | 2 | 0 | 1 | 18 | 9 | 9 | 6 | |
| 3 | Sellebrity | 3 | 2 | 0 | 1 | 4 | 5 | -1 | 6 | |
| 4 | Kapadia Nagar | 3 | 1 | 0 | 2 | 3 | 10 | -7 | 3 | |
| 5 | Carmelites | 4 | 0 | 0 | 4 | 2 | 22 | -20 | 0 |
*Goans S. C. has defeated Mumbai United and Sellebrity.
Group B
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | Mumbai F.C. | 3 | 3 | 0 | 0 | 9 | 2 | 7 | 9 | |
| 2 | Rhema Sports Foundation | 3 | 1 | 2 | 0 | 5 | 4 | 1 | 5 | |
| 3 | Vision Rescue | 3 | 1 | 1 | 1 | 6 | 1 | 5 | 4 | |
| 4 | Steadfast | 3 | 1 | 1 | 1 | 8 | 8 | 0 | 4 | |
| 5 | Indian Football Academy | 4 | 0 | 0 | 4 | 2 | 15 | -13 | 0 |
Group C
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | J.J. Academy | 3 | 3 | 0 | 0 | 11 | 3 | 8 | 9 | |
| 2 | Hegdenar Boys | 3 | 2 | 0 | 1 | 18 | 7 | 11 | 6 | |
| 3 | Desperados | 3 | 2 | 0 | 1 | 4 | 3 | 1 | 6 | |
| 4 | KSP Hydro | 3 | 1 | 0 | 2 | 5 | 13 | -8 | 3 | |
| 5 | Veniza Virar | 4 | 0 | 0 | 4 | 0 | 12 | -12 | 0 |
*J.J. Academy has defeated Hegdenar Boys and Desperados.
Group D
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | Mumbai Warriors | 3 | 3 | 0 | 0 | 22 | 2 | 20 | 9 | |
| 2 | Phoenix Sports | 3 | 3 | 0 | 0 | 18 | 3 | 15 | 9 | |
| 3 | Dadar XI | 3 | 1 | 0 | 2 | 7 | 8 | -1 | 3 | |
| 4 | F.C. Mumbaikar | 4 | 1 | 0 | 3 | 11 | 14 | -3 | 3 | |
| 5 | Mangesh Sports Academy | 3 | 0 | 0 | 3 | 0 | 31 | -31 | 0 |
Group E
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | M.S.S.A. | 3 | 3 | 0 | 0 | 17 | 0 | 17 | 9 | |
| 2 | Sunday Boys | 4 | 3 | 0 | 1 | 7 | 12 | -5 | 9 | |
| 3 | Madanpura F.C. | 3 | 1 | 0 | 2 | 3 | 4 | -1 | 3 | |
| 4 | P.I.F.A. | 3 | 1 | 0 | 2 | 2 | 9 | -7 | 3 | |
| 5 | S.P. Academy | 3 | 0 | 0 | 3 | 1 | 5 | -4 | 0 |
* M.S.S.A. has defeated Sunday Boys.
Group F
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | Salsette | 3 | 2 | 1 | 0 | 4 | 2 | 2 | 7 | |
| 2 | Kenkre F. C. | 3 | 2 | 0 | 1 | 10 | 1 | 9 | 6 | |
| 3 | Bharat F.C. | 4 | 2 | 0 | 2 | 11 | 9 | 2 | 6 | |
| 4 | Young Boys F. C. | 3 | 1 | 0 | 2 | 3 | 9 | -6 | 3 | |
| 5 | Nav Nihal | 3 | 0 | 1 | 2 | 1 | 8 | -7 | 1 |
* Salsette has defeated Kenkre F. C. and Bharat F.C.
Group G
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | I.C.L. | 3 | 3 | 0 | 0 | 8 | 1 | 7 | 9 | |
| 2 | Milan Football Academy | 3 | 2 | 0 | 1 | 9 | 3 | 6 | 6 | |
| 3 | R.C.F. | 3 | 2 | 0 | 1 | 9 | 3 | 6 | 6 | |
| 4 | Shastri Nagar | 3 | 1 | 0 | 2 | 2 | 7 | -5 | 3 | |
| 5 | Youth Soccer Academy | 4 | 0 | 0 | 4 | 2 | 16 | -14 | 0 |
*I.C.L. has defeated R.C.F. * R.C.F. has defeated Milan Football Academy.
Group H
| Position | Team | P | W | D | L | F | A | GD | Pts | |
| 1 | Sagar S.C. | 3 | 3 | 0 | 0 | 9 | 0 | 9 | 9 | |
| 2 | Bombay Gymkhana | 4 | 3 | 0 | 1 | 16 | 1 | 15 | 9 | |
| 3 | Grey Athletic | 3 | 1 | 1 | 1 | 1 | 4 | -3 | 4 | |
| 4 | Maurya F.C. | 3 | 0 | 1 | 2 | 0 | 5 | -5 | 1 | |
| 5 | Mumbai Strikers | 3 | 0 | 0 | 3 | 0 | 16 | -16 | 0 |
*Sagar S.C. has defeated Bombay Gymkhana.
**Teams highlighted in green have already qualified for the Knockout Stage.
