Background The Family Practice Integrated Care Project (FPICP) is a team-based program in Taiwan initiated in 2003. This study investigates the influence of FPICP on the quality of diabetes care. Methods This population-based cohort study used Taiwan’s National Health Insurance Administration data on FPICP (fiscal year 2015–2016, with follow-up duration of one year). Participants included diabetic patients aged ≥30 in primary care clinics. We used conditional logistic regression modeling of patient characteristics and annual diabetes examinations and compared FPICP participants with non-participating candidates. Main outcome measures included completion of annual diabetes examinations, including glycated hemoglobin (A1c), low-density lipoprotein (LDL), urine microalbumin (MAU), routine urinalysis (UR), and fundus examination (FE). Results The sample included 298,208 FPICP participants and 478,778 non-participating candidates. After 1:1 propensity score matching, the examination completion rates for FPICP participants and non-participants, respectively, were 94.4% versus 93.6% in A1c, 84.2% versus 83.8% in LDL, 61.9% versus 60.1% in MAU, 59.2% versus 58.0% in UR, and 30.1% versus 32.4% in FE. Conclusion Our findings indicate that a program like FPICP helps improve the quality of diabetes care through regular examinations of Alc, LDL, MAU, and UR.