The diversity of protein food sources, animal and plant, may be a proxy measure of protein quality and adequate protein nutrition. A population-based sample of 1604 Malaysians aged ≥18 y completed one 24-h dietary recall and a new 29-item protein diversity indicator (PDI). Socio-demographic data were obtained by self-report. Mean total protein intakes were 75.2 g/d from 24-h recalls and 74.9 g/d from PDI. Protein diversity indicator-estimated protein intakes were 36.2% from meat and poultry, 8.8% from fish, 16.0% from eggs and dairy, and 39.0% from plants. Intakes of animal proteins varied with socioeconomic status and ethnicity and were associated with higher protein quality, defined as the adequacy of essential amino acids (EAAs) relative to protein requirements. Protein intakes and protein quality in Malaysia were generally adequate. Protein diversity indicator metrics can complement current methods of dietary assessment and may be useful for monitoring protein diversity and quality in other countries currently undergoing nutrition transition.