Background: During the first three months of the COVID-19 pandemic in the Philippines, there was a supply shortage of hydroxychloroquine and methotrexate. Limited access to medication and the life changes resulting from the COVID-19 pandemic may predispose patients with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE) to disease flares. Objective: This study aimed to investigate self-reported symptoms of disease flares among patients with rheumatoid arthritis or systemic lupus erythematosus during the COVID-19 pandemic. Methods: A total of 512 completed online surveys from patients with SLE or RA were collected. The data included sociodemographic characteristics, self-reported physical symptoms, health service utilization, and availability of hydroxychloroquine and methotrexate. Results: Seventy-nine percent of respondents had lupus, while 21% had RA. One-third of the cohort had contact with their attending physician during the two-month quarantine period prior to the survey. Eighty-two percent were prescribed hydroxychloroquine and 23.4% were prescribed methotrexate; but 68.6% and 65%, respectively, had “irregular” intake of these medicines due to unavailability. The current health status was reported as good by 66.2%; 24% had no symptoms during the two-week period prior to the survey. The most common symptoms experienced were joint pain (51%), muscle pain (35%), headache (26.8%), and skin rash (19.1%). Five percent had a combination of these four most common symptoms. Irregular supply of hydroxychloroquine among patients with SLE (n=323) was associated with more frequent occurrence of muscle pain (40.6% vs 27.9%, p=0.03) or rash (27.4% vs 11.7%, p<0.001). Irregular supply of methotrexate among RA patients prescribed hydroxychloroquine and methotrexate (n=36) was associated with more frequent occurrence of joint pains with or without swelling (73.9% vs 38.5%, p=0.04). Irregular supply of hydroxychloroquine was associated with less frequent occurrence of dizziness (0 vs 66.7%, p<0.001) among RA patients (n=18). Conclusion: In our cohort of RA and SLE, the majority reported at least one symptom that may indicate disease flare. There was a significant association between the irregular supply of hydroxychloroquine or methotrexate with the presence of muscle pain, rash, or joint pains during the 14-day period prior to the survey.