Breed and Burn (B&B) fuel cycle in molten salt reactors (MSRs) qualifies this reactor type as one of the best candidates to be developed for the Gen-IV R&D program. This feature can be approached by employing a closed fuel cycle and application of a molten salt reactor as a spent nuclear fuel burner; the features promise sustainable and clean energy in the future. In this study, a complete package has been developed to calculate core inventory, fuel burnup, and salt clean-up systems of molten salt reactors during their lifetime. To achieve this, the iMAGINE-3BIC package (“iMAGINE 3D-Reg Burnup & Inventory Calculator package”) has been developed in MATLAB R2023a by employing a CINDER90 module of MCNPX 2.7 for burnup-calculation and multi-linear regression method (MLR). The package can estimate the core inventory (concentration of 25 actinides and 245 non-actinides elements) and the burnup of the reactor core during MSR lifetime (up to 100 years) while optimizing the computational resources (time, CPU and RAM), and it can even be hassle-freely executed on standalone PCs in an appropriate time due to its generous database. In addition, the salt clean-up module of the iMAGINE-3BIC package can be employed to evaluate the effects of the salt clean-up system on the above parameters over the MSRs’ lifetime. Finally, the iMAGINE-3BIC package has been applied to an iMAGINE reactor core design (University of Liverpool, UK—chloride-based salt fuel system) and an EVOL reactor core design (CNRS, Grenoble, France, fluoride-based salt fuel system) to evaluate and compare the performance of chloride/fluoride-based salt fuel MSRs from the point of burnup, core inventory, and salt clean-up systems. The results confirm that while a chloride-based salt fuel system has some advantages in less dependency on the salt clean-up system and fewer poisoning elements inventory, the fluoride-based system can achieve higher burnup during the reactor lifetime. The outcome of this study, along with the first part of this article, provides evidence to support the neutronic decision matrix as well as the pros and cons of employing chloride- or fluoride-based fuel systems in MSR cores.