Background: The gold standard for diagnosing sleep bruxism (SB) and obstructive sleep apnea (OSA) is polysomnography (PSG). However, a final hypermotor muscle activity often occurs after apnea episodes, which can confuse the diagnosis of SB when using portable electromyography (EMG) devices. This study aimed to compare the number of SB episodes obtained from PSG with manual analysis by a sleep expert, and from a manual and automatic analysis of an EMG and electrocardiography (EKG) device, in a population with suspected OSA. Methods: Twenty-two subjects underwent a polysomnographic study with simultaneous recording with the EMG-EKG device. SB episodes and SB index measured with both tools and analyzed manually and automatically were compared. Masticatory muscle activity was scored according to published criteria. Patients were segmented by severity of OSA (mild, moderate, severe) following the American Academy of Sleep Medicine (AASM) criteria. ANOVA and the Bland–Altman plot were used to quantify the agreement between both methods. The concordance was calculated through the intraclass correlation coefficient (ICC). Results: On average, the total events of SB per night in the PSG study were (8.41 ± 0.85), lower than the one obtained with EMG-EKG manual (14.64 ± 0.76) and automatic (22.68 ± 16.02) analysis. The mean number of SB episodes decreases from the non-OSA group to the OSA group with both PSG (5.93 ± 8.64) and EMG-EKG analyses (automatic = 22.47 ± 18.07, manual = 13.93 ± 11.08). However, this decrease was minor in proportion compared to the automatic EMG-EKG analysis mode (from 23.14 to 22.47). The ICC based on the number of SB episodes in the segmented sample by severity degree of OSA along the three tools shows a moderate correlation in the non-OSA (0.61) and mild OSA (0.53) groups. However, it is poorly correlated in the moderate (0.24) and severe (0.23) OSA groups: the EMG-EKG automatic analysis measures 14.27 units more than PSG. The results of the manual EMG-EKG analysis improved this correlation but are not good enough. Conclusions: The results obtained in the PSG manual analysis and those obtained by the EMG-EKG device with automatic and manual analysis for the diagnosis of SB are acceptable but only in patients without OSA or with mild OSA. In patients with moderate or severe OSA, SB diagnosis with portable electromyography devices can be confused due to apneas, and further study is needed to investigate this.