Malaysia is considered as one of the countries with the highest novel corona virus (COVID-19) infected cases in Southeast Asia. Recent studies have identified that the air quality of a region also governs the transmission of the virus through pollutants. Hence, a study was conducted to assess the influence of air quality on the COVID-19 pandemic spread in central Peninsular Malaysia and Sabah. An attempt was also made to infer the effect of monsoonal precipitation on air quality. Central Peninsular Malaysia consists of major cities like Kuala Lumpur, Selangor and Putrajaya. These cities are highly populated, with the expansion of industrial activities, rapid urbanisation and greater usage of vehicles has resulted in air quality deterioration. Such conditions have led to related public health issues, compared to Sabah in east Malaysia. In this study, COVID-19 infected cases, air quality index (AQI) and precipitation data were collected from 25 January to August 2020 to infer the relationship of air quality to the pandemic spread before, during and after the implementation of lockdown periods in the country, referred as movement control order (MCO). The lockdown periods fall under various monsoon climate patterns in the country. Interpretation of data reveals that the variation in air quality correlates with the infected cases. Improved air quality was observed during the last phase of MCO with a lesser number of infected cases. The HYSPLIT model was adopted to study the backward air mass trajectories for different time frames to identify the variation in the sources of pollutants reaching the study area. The study determined that the air pollutants have reached the study area from various directions, reflecting a mixed contribution from the ocean and land area. The relationship between high precipitation (during inter-monsoon and SW monsoon) and improved air quality reveals the washout effect of air pollutants. The outcome of this study inferred that the variation of air quality and precipitation rates facilitate the pandemic spread in this region in addition to the other meteorological factors, apart from individual immune capacity and social distancing.