Out of Bandić's multifaceted engagement in politics, the most noted part was his mayoralty of Zagreb, which followed the Croatian Democratic Union's (HDZ) first post-socialist period of government (1990–2000), and exacerbated many existing transitional problems in the city.

His legacy remained controversial due to numerous nepotism and clientelism scandals – which involved many of his associates, including his successor Pavičić Vukičević – budget deficit and soon to mature bonds, and the slow and expensive recovery from the heavily damaging 2020 earthquakes.

Continuing his predecessor, Croatian Democratic Union (HDZ) government's, 1990s pattern of deregulation and abandonment of urban planning,[5][6][7][8] Bandić's mayoralty was characterised by unsustainable projects[9] creating unplanned investment-driven sprawl and causing overbuilding.

[18][14] As a consequence, it failed to achieve its objections, and urban renewal in Zagreb was characteristic of the so-called era of the bulldozer: a discarded approach involving construction of unsustainable luxury housing on the site of former undesirable neighbourhoods and areas.

[51] Bandić would repeatedly put focus on attractive perennial capital projects, while failing to improve Zagreb's aging infrastructure; in 2015, 80,000 households lacked running water and sewerage connections.

[64] Bandić established himself as the person in charge of all aspects of running Zagreb,[65] becoming a spokesman for several controversial projects, one of which was the construction of a shopping mall on a historic Donji grad square.

[66] In 2006, real estate developer Tomislav Horvatinčić, who had made use of Bandić's new urban master plan to build the 17-storey HOTO Tower in 2004, presented a plan for "Life Style Center" (later to become Centar Cvjetni, "Flower Centre"), a 50,000 m2 (540,000 sq ft) mall with a 700-car underground parking garage in Zagreb's pedestrian zone, on the Petar Preradović Square, popularly known as Flower Square (Cvjetni trg).

[80] Notably, police cracked down on a protest in February 2010 opposing the conversion of part of Varšavska Street pedestrian zone to parking garage ramp, arresting its leaders, including Green Action president and future Mayor of Zagreb Tomislav Tomašević and actress Urša Raukar.

[84] A related controversy arose temporarily in 2016, as Bandić administration allowed Horvatinčić to place a bar patio in front of the entrance to the Flower Square's Serbian Orthodox Cathedral, also hindering access to a public seating area.

[108] The project would create a new neighbourhood on a 39.5-hectare (98-acre) area that was to be connected to the city by an extension of Vukovar Street and a new tram line, with numerous amenities such as a library, a kindergarten and a community swimming pool.

[120][121] Bandić was quick to dismiss the issue, lining up with mayor's office employees to drink from an affected hydrant in a publicity stunt,[122] and assuring citizens that the problem would be remedied within days.

[135][136] As part of the confidential concession agreement, the passage of Arena Zagreb into city ownership depends on regular payments of rental fees, which Bandić's administration did not service in timely fashion.

[155] Many projects were criticised for the poor quality of execution, such as an underpass which continued to flood regularly during rainfall despite specific repairs to that end, and the inconsistently marked cycling paths.

[221] Bandić lobbied for the controversial project which involved pedestrian entrances surrounding Ivan Meštrović's monument, Well of Life, while garage ramps would flank the 19th-century building of the Croatian National Theatre.

[229] At the end of the process, Bandić was found not guilty, and subsequently taunted protestors by cutting grass on the square while dressed in the uniform of Zrinjevac, the city's park maintenance company, which caused them to demand his resignation.

Protests, which were ongoing by 2016, intensified in 2017, the election year, by which point Savica residents and activists held round-the-clock sit-ins to prevent construction crews from entering the park.

[253] On 1 January 2007, Bandić founded the Zagreb Holding, placing city companies under a single corporate umbrella, of which he maintained full control as the sole board member until a 2009 intervention by the Ministry of Public Administration.

[259] Little of the money was spent on the intended purpose, being re-routed into patching up the city budget, real estate acquisition, and Sopnica–Jelkovec construction, although Bandić had vouched this would not happen when the bonds were issued.

[53] A 2013 paper called for restructuring Zagreb Holding, finding that the company was exposed to high foreign exchange risk and relied on new loans to pay off existing debts.

[262] ZET, the public transport company, operated at a loss for a long time due to Bandić's decision to allow free travel for most Zagreb citizens, and was criticised for practices such as giving a commission to drivers selling tickets.

[270] Using Benford's law, CRCB found high price distortions compared to true market value of services rendered, especially in no-competition tenders and those issued by Zagreb Holding.

The mayor was charged with evading tax on political donations, illegal preferential treatment of the CIOS refuse management company, as well as trading city-owned land below market price.

In April 2004, then-mayor Vlasta Pavić criticized Bandić for buying land formerly owned by the Zagrepčanka meat packing plant, as the city was unable to register itself as the owner.

[311][312][313] In 2018, Bandić presented a project which would mandate an allegedly newly invented form of HHO cleaning of car engines for all vehicles in Zagreb at cost to owners, in order to reduce their carbon footprint.

Bandić, who multiple times stated that Tuđman would get the "most beautiful square in Zagreb because he deserves it",[323] ultimately gave the president the hitherto unnamed park behind Rudolf barracks,[324] a move criticised by the right.

[347] In March 2020, Bandić was criticised for making jokes about the lack of soap in Zagreb schools, telling students to wash their hands with charcoal ash as he had supposedly done in his youth.

The authorities estimated that 20,000 people, or more than half of residents of Donji grad had moved out of their homes by the middle of April,[370][371] and scaffolding protecting pedestrians from falling masonry began to be erected only in 2021.

[401][266][402] Some measures were reversed in face of financial issues; e.g. Bandić went from offering free rides to everyone in certain conditions in 2008, to vying for massive bus fare hikes in 2010, stating that it was "high time for a fair distribution of subsidies",[264] after ZET, the public transport company, registered a large deficit.

[419] In 2008, a letter signed by 26 public figures of the Croatian Left, including academic Dražen Lalić, criticized the policies of the SDP, particularly Bandić's tenure as mayor and corruption allegations, and called out Milanović for "betraying social democracy".

The SAO tossed the case in February 2022, citing no reasonable grounds for assuming Bandić was not given proper medical care in the moments after suffering the heart attack.