Background: Non-communicable diseases (NCDs) have received political attention and commitment, yet surveillance is needed to measure progress and set priorities. Building on global estimates suggesting that Peru is not on target to meet the Sustainable Development Goal 3.4, we estimated the contribution of various NCDs to the change in unconditional probability of dying from NCDs in 25 regions in Peru. Methods: Using national death registries and census data, we estimated the unconditional probability of dying between ages 30 and 69 from any and from each of the following NCDs: cardiovascular, cancer, diabetes, chronic respiratory diseases and chronic kidney disease. We estimated the contribution of each NCD to the change in the unconditional probability of dying from any of these NCDs between 2006 and 2016. Results: The overall unconditional probability of dying improved for men (21.4%) and women (23.3%). Cancer accounted for 10.9% in men and 13.7% in women of the overall reduction; cardiovascular diseases also contributed substantially: 11.3% in men) and 9.8% in women. Consistently in men and women and across regions, diabetes moved in the opposite direction of the overall reduction in the unconditional probability of dying from any selected NCD. Diabetes contributed a rise in the unconditional probability of 3.6% in men and 2.1% in women. Conclusions: Although the unconditional probability of dying from any selected NCD has decreased, diabetes would prevent Peru from meeting international targets. Policies are needed to prevent diabetes and to strengthen healthcare to avoid diabetes-related complications and delay mortality.