Background Obesity has long been a severe threat to public health as an epidemic, and studies on its pathogenesis and treatment have been ongoing. Our study aims to compare the serum levels of bone morphogenetic protein 1 (BMP1), neuregulin 4 (NRG4), and apolipoprotein A5 (ApoA5) in obese and non-obese individuals and investigate their association with obesity. Methodology Our study included a total of 111 participants, of whom 46 were obese (body mass index (BMI) ≥30 kg/m2), aged 18-65 years, and had no comorbidities, and 65 were non-obese (BMI = 18.5-29.9 kg/m2) without any additional disease. For all participants, BMP1, NRG4, and ApoA5 levels were determined and compared with clinical and biochemical parameters. Results Overall, 60.4% (n = 67) of the participants were female and 39.6% (n = 44) were male. In terms of the BMI scores, 58.6% (n = 65) had a BMI <30 kg/m2 and 41.4% (n = 46) had a BMI ≥30 kg/m2. Both, the BMI and the gender groups did not differ significantly in terms of age (p = 0.093 and p = 0.795, respectively). The weight, fat-free mass, mineral quantity, protein quantity, fluid weight, and fluid ratio values of the male participants were significantly higher than females (p = 0.011, p = 0.001, p = 0.001, p = 0.001, p = 0.001, and p = 0.001, respectively). The aspartate aminotransferase (AST)/alanine aminotransferase (ALT) ratios and the triglyceride/glucose (TG/Glu) ratios were found to be significantly higher in males than in females (p = 0.001 and p = 0.001, respectively). The respective BMP1 (15.88 vs. 13.35), AST/ALT (1.36 vs. 1.04) and TG/Glu ratios (1.47 vs. 1.29) were significantly higher, while the quantitative insulin sensitivity check index (QUICKI) was lower in obese individuals than in non-obese individuals (0.32 vs. 0.34). NRG4 and ApoA5 values were similar between the two groups. BMP1, QUICKI values, and AST/ALT ratios proved to be statistically significant in obesity through the univariable logistic regression analysis (β = 1.066, p = 0.048; β = 0.0001, p = 0.001, and β = 3.707, p = 0.003, respectively). On multiple logistic regression analysis, QUICKI values (β = 0.001, p = 0.001) had a negative and significant effect on obesity, and the AST/ALT ratios (β = 2.803, p = 0.033) had a positive and significant effect on obesity. Conclusions Our study indicates that detecting an important link between BMP1 in obese patients will help elucidate the pathogenesis of obesity and come up with a potential therapeutic candidate. BMP1 levels, along with AST/ALT and TG/Glu ratios, were significantly higher in obese patients. BMP1 levels were also an independent significant predictor of obesity together with AST/ALT ratio and QUICKI in this study, suggesting that it may exhibit a metabolic deterioration in obese individuals. However, the results cannot absolutely tell whether it supported deterioration or was a component of the repair mechanism. Althoughit is generally known from recent studies that BMP1 plays a role in osteogenesis, some encouraging results were obtained in our study indicating that BMP1 may play a role in the pathogenesis of obesity. It is expected that our results will not only promote the elucidation of the pathogenesis of obesity, but also provide a therapeutic agent.