Multispectral imaging captures spatial information across a set of discrete spectral channels and is widely utilized across diverse applications such as remote sensing, industrial inspection and biomedical imaging. Multispectral filter arrays (MSFAs) are filter mosaics integrated atop image sensors that facilitate cost-effective, compact, snapshot multispectral imaging. MSFAs are pre-configured based on application—where filter channels are selected corresponding to targeted absorption spectra—making the design of optimal MSFAs vital for a given application. Despite the availability of many design and optimization approaches for spectral channel selection and spatial arrangement, major limitations remain. There are few robust approaches for joint spectral-spatial optimization, techniques are typically only applicable to limited datasets and most critically, are not available for general use and improvement by the wider community. Here, we reconcile current MSFA design techniques and present Opti-MSFA: a Python-based open-access toolbox for the centralized design and optimization of MSFAs. Opti-MSFA incorporates established spectral-spatial optimization algorithms, such as gradient descent and simulated annealing, multispectral-RGB image reconstruction, and is applicable to user-defined input of spatial-spectral datasets or imagery. We validate the toolbox against the standard hyperspectral datasets Samson and Jasper Ridge, and further show utility on experimentally acquired fluorescence imaging data. In conjunction with end-user input and collaboration, we foresee the continued development of Opti-MSFA for the benefit of the wider research community.