question: BACKGROUND: To assess the completeness of reporting, research transparency practices, and risk of selection and immortal bias in observational studies using routinely collected data for comparative effectiveness research. METHOD: We performed a meta-research study by searching PubMed for comparative effectiveness observational studies evaluating therapeutic interventions using routinely collected data published in high impact factor journals from 01/06/2018 to 30/06/2020. We assessed the reporting of the study design (i.e., eligibility, treatment assignment, and the start of follow-up). The risk of selection bias and immortal time bias was determined by assessing if the time of eligibility, the treatment assignment, and the start of follow-up were synchronized to mimic the randomization following the target trial emulation framework. RESULT: Seventy-seven articles were identified. Most studies evaluated pharmacological treatments (69%) with a median sample size of 24,000 individuals. In total, 20% of articles inadequately reported essential information of the study design. One-third of the articles (n = 25, 33%) raised some concerns because of unclear reporting (n = 6, 8%) or were at high risk of selection bias and/or immortal time bias (n = 19, 25%). Only five articles (25%) described a solution to mitigate these biases. Six articles (31%) discussed these biases in the limitations section. CONCLUSION: Reporting of essential information of study design in observational studies remained suboptimal. Selection bias and immortal time bias were common methodological issues that researchers and physicians should be aware of when interpreting the results of observational studies using routinely collected data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12916-021-02151-w.