Background: Although some studies have explored the effects of responses to COVID-19 on mortality, there are limited data on their effects on more immediate health risk factors and the trends of chronic diseases. Objective: To explore the prevalence of some behavioral health risk factors, intermediate risk factors, and chronic diseases at different timepoints during 2020 using the data available from a currently used surveillance system in Saudi Arabia. Methods: This study undertook a secondary analysis of data from the Sharik Health Indicators Surveillance System (SHISS). The SHISS employs short cross-sectional phone interviews, conducted in all 13 administrative regions of Saudi Arabia on a quarterly basis. Each interview lasts approximately 4 min and is conducted by a trained data collector. The SHISS collects demographic data, as well as data on the major behavioral and intermediate chronic disease risk factors and the major chronic diseases, including diabetes, heart disease, stroke, cancer, and chronic respiratory diseases. Results: Of the 44,782 potential participants contacted in 2020, 30,134 completed the interview, with a response rate of 67.29%. Out of the total participants, 51.2% were female. The mean age was 36.5. The behavioral risk factors in this period exhibited significant changes compared to those in the first quarter (Q1) of 2020, when there were no significant restrictions on daily activities. These significant changes are related to reductions in fruit and vegetable intake (adjusted odds ratio (AOR), 0.23) and physical activity (AOR, 0.483), and a significant increase in e-cigarette use (AOR 1.531). In terms of the intermediate risk factors observed in the SHISS, significant increases in hypercholesterolemia (AOR, 1.225) and hypertension (AOR, 1.190) were observed. Finally, heart disease (AOR, 1.279) and diabetes (AOR, 1.138) displayed significant increases compared to Q1. Conclusions: This study shows some evidence of the impact of responses to COVID-19 on the health of the population in Saudi Arabia. Significant reductions in fruit and vegetable intake and physical activity, and significant increases in e-cigarette use, hypertension, and hypercholesterolemia may increase the burden of chronic diseases in Saudi Arabia in the near future. Thus, continuous monitoring of the health risk factors within the population, and early interventions, are recommended to prevent future increases in chronic diseases.