To assess the adherence to clinical practice guidelines (CPGs) and explore the barriers to their implementation among primary care physicians (PCPs) in Bahrain. A cross-sectional study was conducted using an online survey among physicians working in 20 randomly selected public sector primary health centers in Bahrain. Private-sector physicians and family medicine residents were excluded. Outcome measures were assessing the extent of adherence to CPGs, describing the results in association with work roles, gender, level of formal training, and years of working experience, and investigating the barriers to adhering to CPGs. The subjects were 149 PCPs (consultants, specialists, and general practitioners) working in government primary health centers. The vast majority (98.0%) reported that they implemented CPGs in their daily practice. The most commonly cited reason (79.2%) for implementation was that the CPGs were evidence-based. The most implemented guidelines pertained to diabetes (91.3%), hypertension (81.2%), and hyperlipidemia (69.8%). The least implemented ones were screening of women (38.9%) and postnatal care (45.6%). The level of formal medical training was associated with the implementation of CPGs on preventive care, antenatal and postnatal care, and children and women screening (p < 0.05). Hypertension and bronchial asthma guidelines were implemented more by male physicians (p < 0.05) while female physicians were more adherent to CPGs on antenatal and postnatal care, and women and child screening (p < 0.05). The main barrier reported by the physicians was that they wished to know more about CPGs before applying them (mean ± SD = 3.8 ± 0.9). The perception that managers or directors are non-cooperative towards the application of CPGs was associated with years of experience (p = 0.008) and the position of the physician (p = 0.028). General practitioners were more likely to consider non-cooperation from patients as a barrier (p = 0.025). Most PCPs in Bahrain are adherent to CPGs in their daily practice and encounter minimal barriers. Identifying and resolving barriers can help develop unified and standardized guidelines that promote better consistency in patient management, minimize medical errors, and conserve resources.