The ongoing nutrition transition in lower- and middle-income countries (LMIC) in South East Asia may have a positive impact on protein nutrition. This study assessed the diversity of plant and animal protein food sources in relation to essential amino acid (EAA) adequacy in a population-based sample (N 1665) in Indonesia. Dietary intakes from in-person 24 h recalls provided data on energy and protein intakes (in g/d) from plants (grains, legumes), meat, poultry and fish, and eggs and dairy. Protein diversity scores were based on the number of protein food sources over 24 h. EAA scores were the ratio of amino acid intakes to recommended values. Protein diversity and EAA scores were then compared across multiple socio-demographic indices. Analysis of variance and χ2 tests were used to test for differences among groups. Energy intakes were 1678 kcal/d for men and 1435 kcal/d for women. Average protein intakes (and prevalence of inadequacy) were 59⋅4 g/d (41⋅7 %) for men and 51⋅5 g/d (51⋅1 %) for women. In regression analyses, higher protein diversity scores were associated with higher protein intakes, more animal protein and less plant protein and with higher EAA scores. Lower protein diversity scores were associated with lower intakes of lysine, leucine and valine relative to requirements, as well as with lower EAA, rural settings, less wealth and less modernisation. Greater diversity of animal protein food sources, observed among groups of higher socio-economic status, was linked to better amino acid adequacy and protein nutrition.