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Abstract Background Older adults with multimorbidity represent a growing segment of the population. Metrics to assess quality, safety and effectiveness of care can support policy makers and healthcare providers in addressing patient needs. However, there is a lack of valid measures of quality of care for this population. In the MULTIqual project, 24 general practitioner (GP)-reported and 14 patient-reported quality indicators for the healthcare of older adults with multimorbidity were developed in Germany in a systematic approach. This study aimed to select, validate and pilot core sets of these indicators. Methods In a cross-sectional observational study, we collected data in general practices (n = 35) and patients aged 65 years and older with three or more chronic conditions (n = 346). One-dimensional core sets for both perspectives were selected by stepwise backward selection based on corrected item-total correlations. We established structural validity, discriminative capacity, feasibility and patient-professional agreement for the selected indicators. Multilevel multivariable linear regression models adjusted for random effects at practice level were calculated to examine construct validity. Results Twelve GP-reported and seven patient-reported indicators were selected, with item-total correlations ranging from 0.332 to 0.576. Fulfilment rates ranged from 24.6 to 89.0%. Between 0 and 12.7% of the values were missing. Seventeen indicators had agreement rates between patients and professionals of 24.1% to 75.9% and one had 90.7% positive and 5.1% negative agreement. Patients who were born abroad (− 1.04, 95% CI = − 2.00/ − 0.08, p = 0.033) and had higher health-related quality of life (− 1.37, 95% CI = − 2.39/ − 0.36, p = 0.008), fewer contacts with their GP (0.14, 95% CI = 0.04/0.23, p = 0.007) and lower willingness to use their GPs as coordinators of their care (0.13, 95% CI = 0.06/0.20, p