1. With the use of stable isotopes, new concepts have emerged based on the idea that the ecological niche can be approximated by the isotopic niche defined as a δ-space area with isotopic δ values as coordinates. This study aims to (i) redefine functional indices originally based on quantitative biological traits of species and demonstrate the ecological significance of newly defined isotopic functional indices (IFI) in a δ-isotopic space, (ii) compare IFI using biomass data with existing unweighted isotopic indices using only isotopic compositions. 2. Using a community-wide approach, we tested IFI using isotopic compositions of a large set of associated species from two marine benthic communities widely reported in coastal shallow waters: the common Amphiura filiformis muddy-sand community and the engineered Haploops nirae sandy-mud community. Biomass and isotopic composition (13C and 15N) of all species were measured during four seasons. 3. IFI were calculated in the isotopic space defined by the two communities, and variations were analysed: (i) isotopic functional richness indices measure the overall extent of the community trophic niche. They are higher in the Haploops community due to a higher diversity in food sources but also to longer food chains. (ii) isotopic functional evenness indices quantify the regularity in species distribution and the density in species packing. They showed that the biomass is concentrated at the edges of the food web in the Haploops community, outside the isotopic range of the main food source. (iii) isotopic functional divergence indices quantify the degree to which species distribution maximizes the divergence. They showed a larger utilization of secondary food sources in the Haploops community. 4. The IFI variations responded according to expectations overall, based on the extensive knowledge of those communities. Results highlighted that IFI weighted with species biomass provide new insights into how the structure of energy accumulation as biomass between species is likely to underpin community structure and the interplay between structural components of richness, diversity and evenness of biomass distribution.