Although minimally invasive endoscopic surgery techniques are established standard treatment choices for various degenerative conditions of the lumbar spine, the surgical indications of such techniques for specific cases, such as segments with ossification of the ligamentum flavum (OLF) or calcification of the ligamentum flavum (CLF), remain under investigation. Therefore, the authors aimed to demonstrate the short-term outcomes of minimally invasive endoscopic surgery in patients with degenerative lumbar disease with CLF or OLF. This is a retrospective cohort study including consecutive patients who underwent microendoscopic posterior decompression at the authors' institution, where the presence of OLF and CLF did not influence the surgical indication. Fifty-nine patients with OLF and 39 patients with CLF on preoperative CT were identified from the database. Subsequently, two matched control groups (one each matched to the OLF and CLF groups) were created using propensity scores to adjust for age, sex, preoperative Japanese Orthopaedic Association (JOA) score and Oswestry Disability Index, and diagnosis. The background, surgical outcomes, and changes in clinical scores were compared between the matched groups. If there was a significant difference in the improvement of clinical scores, a multivariate linear regression model was applied. On performing univariate analysis, patients with OLF were found to have a higher body mass index (Mann-Whitney U-test, p = 0.001), higher incidence of preoperative motor weakness (chi-square test, p = 0.019), longer operative time (Mann-Whitney U-test, p < 0.001), and lower improvement in the JOA score (mixed-effects model, p = 0.023) than the matched controls. On performing multivariate analysis, the presence of OLF was identified as an independent variable associated with a poor recovery rate based on the JOA score (multivariate linear regression, p < 0.001). In contrast, there were no significant differences between patients with CLF and their matched controls in terms of preoperative and surgical data and postoperative improvements in clinical scores. Although the perioperative surgical outcomes, including the surgical complications, and the in-hospital period did not significantly differ, the short-term improvement in the JOA score was significantly lower in patients with degenerative lumbar disease accompanied by OLF than in the patients from the matched control group. In contrast, there were no significant differences in the short-term improvement in clinical scores and perioperative outcomes between patients with CLF and their matched control group. Thus, the surgical indications of minimally invasive posterior decompression for patients with CLF can be the same as those for patients without CLF; however, the indications for patients with OLF should be further investigated in future studies, including the other surgical methods.