Besides being the capital city, Kota Kinabalu is also the main industrial and commercial centre for Sabah. The economy is dominated by the primary sector of industry. Historically, the secondary sector dominated the economy, but due to rapid urbanisation and economic development, this sector of economy is slowly diminishing.

More recently, a move towards a more tertiary based industry has become more apparent, especially with regards to the boom in the tourism industry. Many state-level, national-level and international commercial banks, as well as some insurance companies have their headquarters or branches here.

A number of industrial and manufacturing companies also have plants here especially in the industrial districts of Likas, Kolombong, and Inanam. The ongoing construction of the 8,320-acre Kota Kinabalu Industrial Park (KKIP) in Sepanggar is intended to boost the city's industrial and commercial activity making it a major growth centre in East Malaysia, as well for the BIMP-EAGA (Brunei-Indonesia-Malaysia-Philippines East ASEAN Growth Area) region.

Kota Kinabalu also hosts numerous national, regional, and international conferences or trade fairs every year including the biennial Sabah International Expo, the Asia Pacific eTourism Conference by the United Nations Conference on Trade and Development (UNCTAD), the ASEAN Australian Engineering Congress, and many others. These events are normally held at the Sutera Harbour resort.