Impaired glomerular filtration rate is common health problem in diabetic mellitus patients (DM) with hypertension (HTN). It is a major cause of morbidity, mortality, and poor quality of life. There is limited data on the prevalence and associated factors of impaired glomerular filtration among diabetic mellitus patients with hypertension in Ethiopia. Therefore, this study aimed to determine the prevalence of impaired glomerular filtration rate and associated factors among diabetic patients with hypertension in referral hospitals in Amhara Regional State, Ethiopia, 2020. An institution-based cross-sectional study was conducted in Amhara Regional referral hospitals from February 20 to April 30, 2020. Systemic sampling techniques were used to select diabetic mellitus patients with hypertension. Epi data version 3.0 was used to enter the coded data and then exported to STATA 14 for analysis. Glomerular filtration rate was estimated using the equations of collaboration with chronic kidney disease (CKD-EPI), diet modification in renal disease (MDRD-4), and creatinine clearance (CrCl). In bi-variable logistic regression, variables with a p-value of < 0.25 were included in multi-variable logistic regression. Using a 95% confidence interval, variables having a p-value ≤ 0.05 in multi-variable logistic regression were declared as statistically significant variables. In this study, a total of 326 study participants were involved, with a 100% response rate. The prevalence of an impaired glomerular filtration rate among diabetic patients with hypertension was 30.1% (95% CI 25.1%-35.1%), 36.6% (95% CI 30.1%-40.8%) and 45.4% (95% CI 39.9%-50.8%), using the equations CKD-EPI, MDRD-4, and CrCl, respectively. Being ≥ 55 years old (CKD-EPI AOR = 2.9, 95%: 1.5–5.5, MDRD-4 AOR = 2.1, 95% CI: 1.2–3.7, CrCl AOR = 5.9, 95% CI: 3.5–10.1), proteinuria (CKD-EPI AOR = 2.7, 95% CI: 1.4–5.3, MDRD-4 AOR = 1.9, 95% CI: 1.1–3.4, CrCl AOR = 1.7, 95% CI: 1.0-2.9), duration of the disease (≥ 5 years) (CKD-EPI AOR = 7.9, 95% CI: 4.2–13.0, MDRD-4 AOR = 7.4, 95% CI: 4.2–13.0, CrCl AOR = 1.9, 95% CI: 1.2–3.3), a glucose level of ≥ 150 mg/dl (CKD-EPI AOR = 2.3, 95% CI: 1.3–4.4, MDRD-4 AOR = 2.1, 95% CI: 1.2–3.8) were variables significantly associated with impaired glomerular filtration rate. The prevalence of impaired glomerular filtration rate among diabetic mellitus patients with hypertension was high. Independent predictors of impaired glomerular filtration rate were older age, duration of the disease, proteinuria, and higher blood glucose levels.