The present study was conducted to evaluate the protein quality of microalgae species Chlorella vulgaris (CV), Chlorella sorokiniana (CS), and Acutodesmus obliquus (AO) and assess the impact of mechanical cell wall disruption. Male Sprague–Dawley rats, around 156 g after adaptation, were placed in metabolic cages and fed experimental diets that were either protein-free or contained 10% protein solely from one of the undisrupted or disrupted CV, CS, and AO. After 3 days, feces were collected for a period of 5 days and analyzed together with diet samples for crude protein contents. Apparent protein digestibility, true protein digestibility, amino acid score, and protein digestibility-corrected amino acid score were calculated. In vitro protein digestibility was measured using the pepsin–pancreatin method and the in vitro protein digestibility-corrected amino acid score was calculated. The crude protein contents of CV, CS, and AO were 53.5, 50.2, and 40.3%, respectively. The amino acid score of the first limiting amino acid was 1.10, 1.27, and 0.86, true protein digestibility was 64.7, 59.3, and 37.9% and protein digestibility-corrected amino acid score was 0.63, 0.64, and 0.29, respectively, for CV, CS, and AO. Mechanical cell disruption significantly improved protein digestibility without a substantial impact on the amino acid profile and score, resulting in the increase of protein digestibility-corrected amino acid score to 0.77, 0.81, and 0.46, respectively, for disrupted CV, CS, and AO. There was a strong correlation between in vitro protein digestibility and apparent protein digestibility (r = 0.986), and also between in vitro protein digestibility-corrected amino acid score and in vivo protein digestibility-corrected amino acid score (r = 0.994). The results suggest that the CV and CS are acceptable sources of protein for humans and animals and quality can be markedly improved by mechanical cell wall disruption. Additionally, in vitro protein digestibility measured using the pepsin–pancreatin method may be used to screen protein product candidates, save animals, reduce cost, and accelerate product development.