Plant extracts are prone to microbial growth that can lead to microbial-induced corrosion (MIC), a major setback for their performance and stability as corrosion inhibitors. Hence, this work aims to identify the microbes that may cause the ineffectiveness of carica papaya leaf extract (CPLE) as a bio-corrosion inhibitor of cold-rolled mild steel in 0.1 M HCl solution for 48 days at 28℃. Cold-rolled mild steel coupons were immersed in 100 ml of 0.1 M hydrochloric (HCl) acid solution containing 1 g, 2 g, 3 g, 4 g, and 5 g of carica papaya leaf extract (CPLE) for 48 days at 28℃. The gravimetric method was used to determine the coupons' corrosion rate (CR), surface coverage, and inhibition efficiency (IE%) of the CPLE. The functional groups in the CPLE were identified using Fourier Transform Infrared Spectroscopy (FTIR), and the surface appearance of the coupons after immersion was examined using an atomic force microscope (AFM). Gravimetric data showed the coupons dipped in a 0.1 M HCl solution containing 3 g/100 ml of the inhibitor exhibited the highest inhibition efficiency of 87.73%, surface coverage of 0.88, and lowest corrosion rate of 0.00255 mm/day or 0.93 mm/yr, after 48 days at 28℃. In FTIR, transmittance peaks occurred at 1558 cm−1 for amines (-NH) in alkaloid scissoring, 1452 cm−1 for aromatic -C = C in flavonoids, 2932 cm−1 for aliphatic methylene (-CH2) and aldehyde (RCOH) stretching, 1035 and 1077 cm−1 for aromatic-OR in tannin, and 3280 cm−1 for out-of-plane bending of hydroxyl (-OH) in phenolics. Vitamin C (522,940 μg/g), flavonoids (860 μg/g), saponins (637.9 μg/g), terpenoid (48.4 μg/g), phenol (120%μg/g), alkaloid (4.18 μg/g), tannin (59.84%), and glycosides (9.04%) make up the extract's average phytochemical content. AFM presents pits and ridges on the mild steel coupons immersed in 0.1 M HCl solution without the extract. Those immersed in the solutions with varying concentrations of the extract had a passive layer of the CPLE adhering to the surfaces of the coupons thereby preventing the coupon’s direct contact with the acid solution and weight loss. However, over time, microbial growth decreased the efficiency of CPLE due to metabolites. Microbial tests show creamy, irregular and raised bacterial total colony-forming units per gram (Tcfu/g) as 4.6 × 105 Tcfu/g and 1.9 × 107 Tcfu/g in 2 runs. Also, a mixture of white and fluffy appearance and spore formation of fungi population of 4.8 × 105 Tcfu/g and 3.2 × 107 Tcfu/g in 2 Runs made up of Penicillium spp, Coccidioides immitis, Aspergillus flavus, and Fusarium spp, with hyphae, were seen in the solutions containing CPLE.