Kidney transplant recipients (KTRs) are highly susceptible to infections due to chronic immunosuppression. During the COVID‐19 pandemic, their risk of atypical bacterial coinfections may have changed, but this impact remains unclear. This study aimed to assess Mycoplasma pneumoniae (MP) and Chlamydia pneumoniae (CP) coinfection patterns in COVID‐19‐positive KTRs.

We retrospectively analyzed hospitalized patients between December 2017 and January 2025 to assess winter‐month positivity rates of MP and CP. Department‐level associations with COVID‐19 status were examined, and a focused analysis of 228 KTRs compared demographic, clinical, and laboratory data between COVID‐19‐positive and ‐negative groups.

MP and CP‐positive detection rates declined during 2020–2021 but rebounded sharply in the winter of 2022, while other respiratory viruses showed no similar increases. An increased risk of coinfection was particularly associated with the Nephrology, Respiratory, and Emergency Departments, where COVID‐19‐positive patients had significantly higher MP/CP positivity rates. Within the Nephrology Department, KTRs represented the most vulnerable subgroup. Compared with COVID‐19‐negative KTRs, COVID‐19‐positive KTRs showed significantly higher rates of pneumonia on imaging (96.3% vs. 80.9%, p = 0.001), MP infection (37.0% vs. 11.6%, p < 0.001), and CP infection (29.6% vs. 8.8%, p < 0.001). Laboratory test results revealed marked immune impairments in COVID‐19‐positive KTRs, including lower leukocyte, lymphocyte, and monocyte counts, profound depletion of T lymphocyte subsets (CD3⁺CD4⁺, CD3⁺CD8⁺), and reduced natural killer cell counts, while hepatic and renal function indices remained largely comparable.

The winter rebound of MP and CP infections during the epidemic wave of the severe acute respiratory syndrome coronavirus 2 Omicron variant appeared most pronounced among KTRs, especially those with concurrent COVID‐19 infection. The elevated coinfection risk may be explained by combined impairments of adaptive and innate immunity rather than organ dysfunction. These findings underscore the need for heightened surveillance, early diagnostic testing, and tailored preventive strategies for transplant recipients and other high‐risk populations during and after COVID‐19 surges.