Background: Preterm birth is a global public health threat for maternal and child health. Each year, 15 million neonates are born preterm worldwide, with 40% resulting from intrauterine infections. Materials and Methods: This cross-sectional and case–control study was conducted from October to February 2019 at Ruhengeri Referral Hospital. A total of 120 swab samples were collected from 40 women, of which 20 were full-term delivery, while the other 20 were preterm delivery. The three samples, including the placental membranes, amniotic fluids, and fetal membranes, were collected immediately after birth. A sterile cotton swab was used to collect the samples and put into swab Stuart sterile plastic container to avoid sample contamination. Samples were transported in a tightly covered carrier to the clinical microbiology laboratory at INES Ruhengeri for microbiological investigation. Gram staining, culture, and biochemical tests were performed. The independent t-test was used to test for significant differences between the means of the two groups, while the Chi-square test (χ2) was used to test for significant association with microorganisms and intra-amniotic infections. Results: A half of the participants were in the age range of 24–29 years. Non-albicans candida (32.7%) and mold (27.9%) were the predominant microorganisms isolated. Non-albicans candida and mold were common to preterm and full-term samples. Staphylococcus species were observed in placental and fetal membrane samples. Escherichia coli, Klebsiella species, Streptococcus species, and Candida albicans were observed among women with preterm birth samples. There was a statistically significant difference between the two means in the amniotic fluid isolates (t = 4.023, P < 0.007), placental membrane isolates (t = 7.17, P < 0.0004), and fetal membrane isolates (t = 6.7, P < 0.0006). Association with microorganisms and intra-amniotic infection was statistically significant with E. coli (χ2 = 3.98, P < 0.05), Streptococcus species (χ2 = 5.53, P < 0.019), non-albicans candida (χ2 = 8.37, P < 0.004), and C. albicans (χ2 = 3.98, P < 0.05). Conclusions: Invasion of the amniotic fluid, placenta, and fetal membranes by pathogenic microorganisms may be associated with the incidence of preterm labor and birth. Early diagnosis is recommended to avoid both maternal and fetal complications.