More importantly the club embarked on a successful run in New Zealand sport's oldest knockout competition, the Chatham Cup.
1989 proved to be a quieter year for the club only finishing 8th in the National league and played poorly in their third round match away to Mount Albert-Ponsonby, losing 1–0.
The club had a resurgent season, finishing the National League in fourth place, two points behind Christchurch United.
In the Chatham Cup the club had an improved run, being knocked out by eventual champions Mount Wellington away 2–1 in the quarter-finals.
This form was carried through into 1991 where the club improved its league position finishing third behind Christchurch United (1st) and Mirimar Rangers.
It did not fare as well in the previous in the Chatham Cup being knocked out by rivals Mount Maunganui away at Links Avenue 3–0 in the fifth round.
It won this game 1–0 and met Waitakere again in the final which was played at Bill McKinlay Park, Auckland.
It fared no better in the Chatham Cup being knocked out at home in a memorable game against Central United in the third round.
Extra time passed with no goals leading to a penalty shootout, won by Waikato 5–4 and thus qualifying for the final.
In the Chatham Cup Waikato made it to the fifth round after wins against Tauranga City and local rival and future merge partner Melville.
This league was innovative in that instead of being played in winter was brought forward to a January start date and the clubs involved were invited to take part, there was no promotion or relegation.
On the Eagle Airways flight back to Hamilton an unnamed player decided to run naked on the plane.
The club's most successful striker this season, Darren Brown ended up 3rd in the leagues golden boot standings with 13 goals.
Muir park was sold to a developer and the funds generated were put aside for the construction of a new top level Waiakato football ground (as of 2021 this has still yet to happen).
The amalgamation with Melville was still in process as the club had to play but all its players had moved on so a team of retirees took to the field in Ngāruawāhia.
They held their own briefly but the difference in fitness and age soon told and Waikato went on to lose its very final game 8–0, producing the club's worst ever defeat to a team it would normally walk through.
Melville and Waikato were officially amalgamated by November 2006, in time for the start of the National Summer League.