Objective: This study aimed to detect and categorize the microorganisms of customized abutments returned from laboratories due to probable contamination and their role in peri-implantitis. Methods: The samples included 202 abutments from 10 laboratories. Ten μL aliquots obtained from the microbial suspension of each abutment were inoculated on sheep blood agar (as non-selective enriched media), MacConkey agar (selective media for Gram-negative bacteria), Columbia agar with colistin and nalidixic acid agar (selective media for Gram-positive bacteria) and Sabouraud Dextrose Agar with antibiotics (selective media for fungi). They were then incubated in an aerobic atmosphere at 37°C. The molecular methods based on 16S rRNA gene sequence analysis were used in the identification of isolates that did not fit with any recognized biochemical profiles. The distribution of qualitative variables was presented numerically and according to frequency. Complex sample analysis with a 95% confidential interval was used for analysis. Results: From a total of 49 detected microorganisms, 44 were aerobic bacteria and 5 were fungi. Micrococcus luteus, Bacillus subtilis, Staphylococcus epidermis and Candida (the dominant genus among fungi) were the dominant species observed in samples from all 10 laboratories, and on average presented on 13.7, 6.2, 5.0 and 4.1 abutments, respectively. The most abundant Gram-positive and Gram-negative bacteria were M. luteus and Acinetobacter baumannii, respectively. B. subtilis was the most common bacillus, and M. luteus was the most common coccus. Conclusions: Certain decontamination protocols and regulations must be defined to eliminate bacteria and fungi, as both were present in samples from all of the laboratories.