There are care gaps in the evaluation and treatment of osteoporosis after a fragility fracture. The Joint Commission is considering adoption of core measures. We compared compliance between two secondary fracture prevention programs in our institution. Incorporating strengths of both may provide the best outcomes for secondary fracture prevention. Purpose There are significant care gaps in the evaluation and treatment of osteoporosis after occurrence of fragility fracture. The Joint Commission is considering adoption of a core measure set on osteoporosis-associated fractures, including laboratory assessment, bone density testing, and osteoporosis pharmacologic therapy. We compared compliance to these proposed measures between two secondary fracture prevention programs in patients hospitalized for acute fracture in an open medical system. Methods We conducted a retrospective, single center medical records review of a nurse practitioner-led Fracture Liaison Service (FLS), a physician-led Fracture Prevention Program (FPP), and a historical time without any secondary fracture prevention program (Usual Care) for baseline care. Primary outcomes were the completion of five laboratory tests (calcium, 25-hydroxy vitamin D, renal function, liver function, and complete blood count), order placement and completion of dual x-ray absorptiometry (DXA) scan within 3 months, prescription of osteoporosis medication within 3 months, and medication adherence at 6 months after hospital discharge. Results Completion of all five laboratory tests was higher in FPP versus FLS (84.7 vs. 36.9%, p < 0.001). DXA scan completion was higher in FPP than FLS but not statistically significant (66.7 vs. 54.9%, p = 0.11). Medication prescription at 3 months and adherence at 6 months were significantly higher in FPP versus FLS (65.3 vs. 24.0%, p < 0.001 and 70.8 vs. 27.7%, p < 0.001, respectively). Conclusion Incorporating strengths of both FLS (care coordination) and FPP (physician direction) may provide the best outcomes for secondary fracture prevention by ensuring laboratory and DXA testing and initiating osteoporosis medication.