The body mass achieved by juveniles before reaching independence is a key predictor of viability and fitness in many animals. While variation in the body mass of juveniles may be explained by a plethora of genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. However, the gut microbiota is known to change during development and it is not clear whether microbiome predicts fitness, and if it does, whether this is reflective of current or future condition. We collected data on nestling weight and survival to fledging as key traits associated with animal fitness. We investigated temporal associations between great tit gut microbiome and fitness across development by sampling nestling faeces as a proxy for gut microbiome at day 8 and day 15 post-hatching. We also investigated whether particular microbial taxa were ‘indicator species’ for birds that survived, and birds that did not survive. There was no link between contemporary weight and microbial diversity at day 8 or day 15. However, weight at day 15 was negatively associated with gut microbial diversity at day 8. Three Lactobacillaceae spp. were identified as ‘indicator species’ for birds that survived, and at least one of which was also associated with future weight gain, suggesting that some Lactobacillaceae taxa could be used as a marker for predicting natal viability. We highlight that microbial-host fitness effects should be investigated longitudinally as there may be critical development windows in which key microbiota are established and prime host traits associated with nestling growth such as digestive and/or immune functions. Pinpointing which features of the gut microbial community impact on host fitness, and when, will shed light on evolutionary processes and inform conservation practices.