Host associated probiotics (HAPs) provide health benefits to the host when administered as dietary supplement. However, a short-term probiotics application strategy has yet to be optimized. A 90-days study was conducted to evaluate the response of Malaysian mahseer, Tor tambroides post larvae fed with basal diet enriched HAPs for 30-days, and its response following another 60-days feeding with only basal diet. Three experimental diets (Enterococcus faecalis strain 2674 (T1), Aeromonas sp. strain A8-29 (T2) and E. faecalis strain FC11682 (T3)) were prepared by spray-coating each HAPs on a basal diet at 1 × 108 CFU/g feed. Differences in growth performances, whole-body proximate and fatty acid composition, muscle morphometry, and gut morphology were evaluated. Results showed that after 30 days, T3 fish produced highest growth. All HAP treatment groups showed better muscle distribution profile, improved fatty acid composition, and higher villus length, width and area, than control group. After 90 days, the growth of T3 fish was still the highest. Muscle distribution profile and villus growth were higher in HAP treatments, although only total n-6 PUFA, total MUFA, linoleic acids, and linolenic acids in HAP treated fish remained high after probiotics withdrawal. No difference in whole-body proximate composition was observed in both 30 and 90 days. Collective findings demonstrated that short-term application of HAPs at an early stage could be used to boost T. tambroides growth, with E. faecalis strain FC11682 showing the best efficacy.