During this era, the Blues played the majority of their home matches at Eden Park, with round robin fixtures occasionally held at Growers Stadium in Pukekohe.

In 1996 the side won eight of eleven round robin matches and finished the regular season in second place (behind the Queensland Reds on 41 points.

Although in the seasons leading up to the trade North Harbour and Northland had outperformed Counties Manukau and Thames Valley in provincial rugby (thus potentially widening the already sizeable gap between the Blues' and Chiefs' on-field performance), it enabled both teams to represent unions in closer geographical proximity.

[citation needed] The expanded 14 team competition could not have started worse for the Blues, who were in 2006 forced by the NZRU to include North Harbour captain Rua Tipoki in their squad of 24 players who are 'protected' from the draft.

In 2009, Pat Lam was appointed as coach, however the team was not able to make significant improvements under his leadership for the remainder of Super 14, missing the playoffs in both the 2009 and 2010 seasons.

The team subsequently defeated the New South Wales Waratahs 26 – 13 to secure a semi-final against the Queensland Reds in Brisbane, which they lost 30–13.

[5] 2012, the team's fourth season under coach Pat Lam, saw the arrival of former Hurricanes icons, and 2011 Rugby World Cup winners, Ma'a Nonu and Piri Weepu.

[6] In the same match, Rene Ranger became the first Blues player to receive a white card, which resulted in a two-week suspension.

Growing frustration among fans was evident during this period, with racist remarks directed at coach Pat Lam via social media, talkback radio and the Blues own website.

[7][8] Lam, who is of Samoan descent, received support from a number of former Blues players during this period, including Michael Jones and Eroni Clarke.

[10] The 2013 season saw an all new Blues team with many players leaving, including Ma'a Nonu to the Highlanders[11] and Gareth Anscombe to the Chiefs.

[12] On the morning of 31 October 2012 new coach Sir John Kirwan announced the 2013 Blues squad which included 14 Super Rugby debutants, and Ali Williams taking over as captain.

Beating the Highlanders at home and completing the double over the Hurricanes with a 28–6 win at Eden Park before losing a close game against the Reds.

The Blues walked off the field to a standing ovation from their fans, the first time an Eden Park crowd had been upstanding for a defeat.

This also included former National Rugby League (NRL) player Benji Marshall who had previously played with the Wests Tigers for 10 years.

They returned to Eden park to defeat the Hurricanes, followed by a bonus point win in Perth against the Western Force.

[18] Ihaia West, Patrick Tuipulotu, Benji Marshall, and Tom Donnelly all made their Super Rugby debut for the Blues in the 2014 season.

The end of the season was marked by the resignation of coach Sir John Kirwan, who had been with the team for the last three years winning just 17 out of 58 games.

Dominant wins against the Brumbies (40–15) and Waratahs (34–28) showed that the Blues could still be highly competitive, however their last-place conference finish left them outside the qualification pool for the season´s semi-finals, with rival New Zealand franchise the Hurricanes emerging the eventual champions.

Crushing losses to the Hurricanes (42–24) and Crusaders (54–17) in the last two rounds illustrated how far the team´s performances had collapsed from coach Tana Umaga´s first, relatively respectable season in charge, and emphasized the need for structural reform at the club.

MacDonald´s first year in charge saw little in the way of definite improvements to the Blues win–loss record, with only 5 wins from 17 games giving them their sixth consecutive last-place finish in the New Zealand conference.

While their overall standards had improved, their margins of both victory and defeat remaining consistently low, the Blues were unable to mount much of a challenge that season.

The Gordon Hunter Memorial Trophy is contested between the Blues and Highlanders as a part of regular season fixtures between the two sides.

The team's primary home ground is Eden Park, located in the central Auckland suburb of Kingsland.

As of 2021 60% of the club is owned (divided 65%, 29% and 6%) by the three unions, through Rugby Holdings Ltd., and 40% by private consortium Better Blues Company Limited.

Don Mackinnon, also a former New Zealand Netball and High Performance Sport NZ director, took over in 2019 as Blues Chairman from Tony Carter who chaired the board since it became a stand-alone organisation in 2013.

The current board includes John Hart, Sam Lotu-liga, Richard Dellabarca, Kate Daly, Grant Graham and Brian Wilsher.

Hore beat off serious competition from 70 applicants to become Blues CEO and believes glory days can return to the team's home ground of Eden Park.

The final round match between the Crusaders and Blues was cancelled due to Covid-19 restrictions, with each team receiving 2 competition points.

[30][31][32] ^4 Super Rugby Aotearoa adopted the same format in 2021 as the inaugural tournament in 2020, with the addition of a final between the top two ranked teams at the conclusion of the round robin stage.