Background The simultaneous or intermittent use of alternative treatments and prescription medications for hypertension and type 2 diabetes mellitus can have adverse health effects. Objectives To identify beliefs and practices associated with the use of alternative treatments for hypertension and type 2 diabetes mellitus among patients. Methods A mixed-methods study including an investigator-administered survey and focus group discussion sessions using convenience sampling was conducted among patients aged ≥18 years during May to August 2018. Descriptive statistics were used to describe and compare demographic characteristics among groups of survey participants using JMP Pro 14.0. Thematic analysis was conducted to analyze the qualitative data using NVivo. Results Most study participants (87-90%) were on prescription medication for their condition. Of survey participants, 69% reported taking their medication as prescribed and 70% felt that prescription medicine was controlling their condition. Almost all participants (98%) reported using alternative treatments, mainly herbal medications, and 73-80% felt that herbal medicines controlled their conditions. One-third believed that herbal medicines are the most effective form of treatment and should always be used instead of prescription medication. However, most participants (85%) did not believe that prescription and herbal treatments should be used simultaneously. Most (76-90%) did not discuss herbal treatments with their healthcare providers. Four themes emerged from the focus group sessions: 1) Simultaneous use of herbal and prescription medicine was perceived to be harmful, 2) Patients did not divulge their use of herbal medicine to healthcare providers, 3) Alternative medicines were perceived to be highly effective, and 4) Religiosity and family elders played key roles in herbal use. Conclusions This study provides useful insights into perceptions and use of alternative treatments by patients that can be used by healthcare providers in developing appropriate interventions to encourage proper use of prescription medicines and alternative medicines resulting in improved management of these chronic diseases.