Background: Helicobacter pylori infection is the most common chronic bacterial infection and there were approximately 4.4 billion individuals with H pylori infection worldwide. Among those, hundreds of millions of people develop peptic ulcer disease during their lifetime and still tens of millions might progress to gastric cancer. Hence, early information is very important to prevent upper gastrointestinal complications. Consequently, the current study aimed to assess the magnitude and associated risk factors of Helicobacter pylori infection among adult dyspeptic patients attending Bokoji hospital, Southeast Ethiopia. Methods: A hospital-based cross-sectional study involving 348 adult dyspeptic patients attending Bokoji hospital was carried out from July 16 to October 31, 2019. About 50 mg of fresh stool and 60 µl of capillary blood were collected from each dyspeptic patient and analyzed for detection of Helicobacter pylori antigens, presence of intestinal parasites and ABO blood grouping respectively. Data were entered using Epi Info 7 and Statistical analysis was done using SPSS version 21 and a p-value less than 0.05 was considered as statistically significant. Results: The overall magnitude of Helicobacter pylori infection was 47.7%. The magnitude of H. pylori infection was almost two times higher in patients who do not have a habit of handwashing after toilet visit than those who wash their hand's habit of handwashing after visiting toilet (AOR 2.241, 95% CI (1.410, 3.563) and alcohol drinking habit (AOR 1.796, 95% CI (1.087, 2.968). Conclusions: The magnitude of H. pylori was high in the study area and associated with handwashing habits after toilet use and alcohol drinking habits. Therefore, the community could be educated on the handwashing habit to minimize H. pylori infections.