Background: Clinical trials evaluating the effect of probiotics on cardiovascular intermediate outcomes have been scarce in recent years. We systematically evaluated the efficacy of probiotics on intermediate cardiovascular outcomes in patients with overweight or obesity. Methods: We searched for randomized controlled trials (RCTs) in four databases (until August 2021) that evaluated the effects of probiotics versus controls on intermediate cardiovascular outcomes. The outcomes were body mass index (BMI), weight, systolic blood pressure (SBP), diastolic blood pressure (DBP), glucose, low-density lipoprotein (LDL), and high-density lipoprotein (HDL) levels. Inverse variance random effects meta-analyses were used. The effects were reported as mean difference (MD), with their 95% confidence intervals (95% CI). The quality of evidence (QoE) was assessed with GRADE (grading of recommendations, assessment, development and evaluations) methodology. Results: A total of 25 RCTs were included (n = 2170), with a range of follow-up from two to six months. Probiotics likely reduced BMI (MD −0.27 kg/m2, 95%CI: −0.35 to −0.19; 17 RCTs; I2 = 26%, QoE: moderate), as well as likely reduced weight (MD −0.61 kg, 95%CI: −0.89 to −0.34; 15 RCTs; I2 = 0%, QoE: moderate), and may have slightly reduce LDL (MD −4.08 mg/dL; 95%CI: −6.99 to −1.17; 9 RCTs; I2 = 87%, QoE: low) in comparison to the controls. However, probiotics had no effect on SBP (MD −0.40 mmHg; 95%CI: −5.04 to 4.25; 7 RCTs; I2 = 100%, QoE: very low), DBP (MD −1.73 mmHg; 95%CI: −5.29 to 1.82; 5 RCTs; I2 = 98%, QoE: very low), glucose (MD −0.07 mg/dL; 95%CI −0.89 to 0.75; I2 = 96%, QoE: very low), HDL (MD −1.83 mg/dL; 95%CI: −4.14 to 2.47; 14 RCTs; I2 = 98%, QoE: very low), or triglycerides (MD −3.29 mg/dL, 95%CI −17.03 to 10.45; 14 RCTs, I2 = 95%, QoE: very low) compared to control arms, and the evidence was very uncertain. Conclusions: In obese or overweight patients, BMI, weight, and LDL were lower in patients who received probiotics compared to those who received controls. Other lipids, glucose, and blood pressure were not affected by the probiotics.