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The non-premixed filtered tabulated chemistry for large eddy simulations employs numerical filtering to resolve a thin flame front on practical LES numerical grids. The flame structure is modified to be coherent with the domain discretization. The first turbulent combustion application of the non-premixed filtered tabulated chemistry approach is presented. A keen comparison of the flamelet filtering transformation in the premixed and non-premixed regimes is carried out. Three distinctive features are outlined: the flame thickness variation, the filtered manifold transformation, and the model activation dependence on the chosen diffusion flamelet configuration for a non-premixed filtered approach. The model performance is assessed on two real turbulent flame configurations, Sandia flames D and E, employing a three-dimensional tabulation strategy, where the numerical grid is coupled with the model by the third parameter, i.e., the computational cell size. The repercussions of the above cited aspects are carefully assessed. The results demonstrate that the formalism coupling with an SGS modeling function can adequately describe wrinkled flame front effects. The predictions for both the major stable species and the minor ones accurately correspond with the underlying physics. It turns out that there is a substantial variation of the filter effect as a function of the strain rate of the flame and the considered species. The varying filter sensitivity along the manifold influences the response of the model correction terms and the retrieved variables. The non-premixed FTACLES formalism possibilities and conditions for the model’s utilization and optimal performance are clearly stated, to confirm the idea that SGS closure in diffusive combustion can be derived based on filtering arguments, and not only based on statistical approaches.