Background: Type 2 diabetes (T2DM) is a chronic condition with a high disease burden worldwide, and individuals with T2DM often have other morbidities. Understanding the local multimorbidity profile of patients with T2DM will inform precision medicine and public health, so that tailored interventions can be offered according to the different profiles. Methods: An analysis was conducted of electronic health records (2016–2021) in one hospital in Lima, Peru. Based on ICD-10 codes and the available measurements (e.g., body mass index), we identified all T2DM cases and quantified the frequency of the most common comorbidities (those in ≥1% of the sample). We also conducted k-means analysis that was informed by the most frequent comorbidities, to identify clusters of patients with T2DM and other chronic conditions. Results: There were 9582 individual records with T2DM (mean age 58.6 years, 61.5% women). The most frequent chronic conditions were obesity (29.4%), hypertension (18.8%), dyslipidemia (11.3%), hypothyroidism (6.4%), and arthropathy (3.6%); and 51.6% had multimorbidity: 32.8% had only one, 14.1% had two, and 4.7% had three or more extra chronic conditions in addition to T2DM. The cluster analysis revealed four unique groups: T2DM with no other chronic disease, T2DM with obesity only, T2DM with hypertension but without obesity, and T2DM with all other chronic conditions. Conclusions: More than one in two people with T2DM had multimorbidity. Obesity, hypertension, and dyslipidemia were the most common chronic conditions that were associated with T2DM. Four clusters of chronic morbidities were found, signaling mutually exclusive profiles of patients with T2DM according to their multimorbidity profile.