• MF and NF can effectively separate secondary metabolites of Fusarium solani from fermentation broth. • Bostrycoidin was rejected by 97.5% by microfiltration and purified to 94.1% • Fusarubin, anhydrofusarubin and javanicin was concentrated in the retentate using nanofiltration. • Long term microfiltration experiments showed a stable steady-state flux of 12 L/(m 2 h). • Membrane based unit processes may play an attractive role in large scale biosynthetic pigment production. The use of fugal secondary metabolites is extensive throughout several industries, and the compounds are often extracted using loads of harmful organic solvents. The issues with several different and also similar products produced by the same biosyntethic pathways are challenging the downstream separation and purification, especially when scaling up production for the industry. The main objective of this study was to investigate the separation, concentration and purification possibilities of four different valuable fungal pigments produced by Fusarium solani. We present a full membrane based filtration train to elucidate which membrane type can be useful in the separation and concentration of the compounds. This visualized the possibility if using microfiltration to concentrate bostrycoidin and also to separate fusarubin from the rest of the pigments. Also, a comparison study between three types of microfiltration membranes is presented, showing little to none difference in the investigated membranes. Lastly, a high concentration- high recovery filtration study is presented, concentrating bostrycoidin in an even higher concentration. It is shown in this paper, that it is possible to use membrane filtration to separate, concentrate and purify the fusarubins investigated.