In this research, we analyzed COVID-19 distribution patterns based on hotspots and space–time cubes (STC) in East Java, Indonesia. The data were collected based on the East Java COVID-19 Radar report results from a four-month period, namely March, April, May, and June 2020. Hour, day, and date information were used as the basis of the analysis. We used two spatial analysis models: the emerging hotspot analysis and STC. Both techniques allow us to identify the hotspot cluster temporally. Three-dimensional visualizations can be used to determine the direction of spread of COVID-19 hotspots. The results showed that the spread of COVID-19 throughout East Java was centered in Surabaya, then mostly spread towards suburban areas and other cities. An emerging hotspot analysis was carried out to identify the patterns of COVID-19 hotspots in each bin. Both cities featured oscillating patterns and sporadic hotspots that accumulated over four months. This pattern indicates that newly infected patients always follow the recovery of previous COVID-19 patients and that the increase in the number of positive patients is higher when compared to patients who recover. The monthly hotspot analysis results yielded detailed COVID-19 spatiotemporal information and facilitated more in-depth analysis of events and policies in each location/time bin. The COVID-19 hotspot pattern in East Java, visually speaking, has an amoeba-like pattern. Many positive cases tend to be close to the city, in places with high road density, near trade and business facilities, financial storage, transportation, entertainment, and food venues. Determining the spatial and temporal resolution for the STC model is crucial because it affects the level of detail for the information of endemic disease distribution and is important for the emerging hotspot analysis results. We believe that similar research is still rare in Indonesia, although it has been done elsewhere, in different contexts and focuses.