Abstract Removing filtration and crystallization provides amino acids with reduced purity because Corynebacterium glutamicum cell mass (CGCM) is not removed. This study aimed to evaluate nutritional and functional values of granulated Threonine (Thr) and Valine (Val) with CGCM in diets for growth performance, jejunal mucosa-associated microbiota, nutrient digestibility, and health of nursery pigs. Seventy-two newly weaned pigs (28 d-of-age; initial body weight (BW) of 8.2 ± 0.4 kg) were allotted to 9 treatments (n = 8) based on a randomized complete block design with sex and initial BW as blocks. Treatments consisted of a basal diet with different levels of standardized ileal digestible (SID) Thr and Val: NC (SID Thr and SID Val at 70% of NRC requirement), CT (95% SID Thr using crystalline Thr); CV (95% SID Val using crystalline Val); PT (95% SID Thr using ThrPro); PV (95% SID Val using ValPro); HCT (5 × crystalline Thr used in CT); HCV (5 × crystalline Val used in CV); HPT (5 × ThrPro used in PT); HPV (5 × ValPro used in PV). Diets were fed to nursery pigs for 25 d in 2 phases (10 d and 15 d, respectively). Feed intake and BW were recorded at the end of each phase. Blood samples were collected to measure serum proteins, metabolites, and electrolytes on d 21. Pigs were euthanized at d 25 to collect liver and jejunal tissues for morphological evaluation and jejunal mucosa to measure intestinal health biomarkers. Data were analyzed by SAS using MIXED procedure. Pigs with 95% SID Thr or 95% SID Val tended to have greater average daily gain (P = 0.078) and gross energy digestibility (P = 0.058), had greater (P < 0.05) jejunal villus height, and had lower (P < 0.05) plasma urea nitrogen and liver fibrosis than pigs with 70% SID Thr or 70% SID Val, respectively. Pigs fed a diet with HAAPro had increased (P < 0.05) alpha diversity of jejunal mucosa-associated microbiota than pigs fed a diet with AAPro. Pigs fed a diet with HAAPro had increased (P < 0.05) relative abundance of Bifidobacterium and decreased (P < 0.05) relative abundance of Comamonas than pigs fed a diet with AAPro. In conclusion, increasing the supplementation of AAPro by five folds than typical level did not negatively affect growth performance whereas beneficially modulated the jejunal mucosa-associated microbiota. Results suggest that AAPro can effectively replace the use of crystalline amino acids in pig diets whilst potentially reducing feed costs due to reduced cost of producing such amino acids.