Diabetes mellitus (DM) is a risk factor for pancreatic ductal adenocarcinoma (PDAC) that promotes the promoter methylation of CDH1. It is still unclear whether DM can exert other epigenetic effects, such as altering microRNA (miR) expression, in PDAC. The expression of miR‐100‐5p is known to be changed in DM patients and can suppress the expression of E‐cadherin. In this study, the correlation between DM status and dual epigenetic changes was evaluated in PDAC specimens from patients who underwent radical surgical resection. A total of 132 consecutive patients with PDAC were clinicopathologically evaluated. E‐cadherin and nuclear β‐catenin expression was measured using immunohistochemistry. DNA and miRs were extracted from the main tumor site on formalin‐fixed paraffin‐embedded tissue sections. TaqMan miR assays were applied to assess miR‐100‐5p expression. Bisulfite modification was conducted on the extracted DNA, which was then subjected to methylation‐specific polymerase chain reaction. Immunohistochemistry revealed that decreased E‐cadherin expression and increased nuclear β‐catenin expression were significantly associated with DM and poor tumor cell differentiation. The presence of long‐duration DM (≥3 years) was a significant factor contributing to CDH1 promoter methylation (p < 0.01), while miR‐100‐5p expression was proportionally correlated with the preoperative HbA1c level (R = 0.34, p < 0.01), but not the duration of DM. The subjects with high miR‐100‐5p expression and CDH1 promoter methylation showed the highest level of vessel invasion and prevalence of tumor size ≥30 mm. PDAC subjects with dual epigenetic changes showed poorer overall survival (OS) than those with a single epigenetic change. miR‐100‐5p expression ≥4.13 and CDH1 promoter methylation independently predicted poor OS and disease‐free survival (DFS) in the multivariate analysis. OS and DFS worsened in DM subjects with both HbA1c ≥ 6.5% and DM duration ≥3 years. Thus, DM is associated with two modes of epigenetic change by independent mechanisms and worsens prognosis.