A feeding trial was conducted for 60 days to study the effect of dietary protein, microbial phytase and citric acid on intestinal digesta pH, bone ash and bone mineral contents in Labeo rohita juveniles. Eight experimental diets were prepared in 2 × 2 × 2 factorial arrangement with crude protein levels (25% and 35%), microbial phytase (0 and 500 U kg−1), and citric acid (0 and 3%). The 25% crude protein level feed was supplemented with phytase (U kg−1) and citric acid (%) at the level of 0,0 (C25); 500,0 (T1); 0,3 (T2); 500,3 (T3), and 35% crude protein level feed at 0.0 (C35); 500,0 (T4); 0,3 (T5) and 500,3(T6) respectively. One hundred and twenty juveniles of L. rohita (av. wt. 12.61–13.72 g) were distributed randomly in eight treatments, each of with three replicates. Addition of citric acid in the 25% crude protein feed significantly decreased (P<0.001) feed pH with concurrent decrease in intestinal digesta pH (P<0.001) and increased the bone ash content (P<0.05) by 4.6%. An interaction between citric acid and phytase (P<0.05) was also observed for bone ash content. Increasing the dietary protein content from 25% to 35% significantly decreased (P<0.01) bone Zn content by 14.9%, which was more prominent with the addition of citric acid, resulting in significant interaction between protein and citric acid (P<0.05), but the bone Cu content was significantly increased (P<0.01) with increasing dietary protein content. Dietary supplementation of microbial phytase (500 U kg−1) significantly increased (P<0.05) bone Na, Ca, K, P and Fe contents by 15%, 12.1%, 17.4%, 9.2% and 40.7%, respectively, whereas bone P and Mn content was significantly increased (P<0.05) by addition of citric acid (3%). Addition of phytase to plant‐based diets increased the bioavailability of minerals, thereby increasing bone mineralization. The effect of phytase was increased because of addition of citric acid (3%).