In this work, a cascade approach to obtain different valuable fractions from lemon peels waste was optimised using microwave-assisted processes. Microwave-assisted hydrodistillation (MAHD) with a Clevenger apparatus was firstly used to obtain the lemon essential oil (LEO). The remaining residue was then submitted to microwave-assisted extraction (MAE) to extract the lemon pigment (LP). A Box–Behnken design was used to evaluate the influence of ethanol concentration, temperature and time in LP extraction in terms of extraction yield and colour intensity. Optimal extraction conditions for LP were 80% (v/v) ethanol, 80 °C and 50 min, with a liquid-to-solid ratio of 1:10. The obtained yields for LEO and LP were around 2 wt.% and 6 wt.%, respectively. The composition of LEO was analysed by gas chromatography with flame ionisation detection (GC-FID), and limonene (65.082 wt.%), β-pinene (14.517 wt.%) and γ-terpinene (9.743 wt.%) were mainly identified. LP was purified by using different Amberlite adsorption resins (XAD4, XAD7HP and XAD16N), showing XAD16N the best adsorption capacity. Enrichment factors of 4.3, 4.5 and 5.0 were found for eriocitrin, diosmin and hesperidin, respectively, which were detected as the main components in LP by ultra-high-performance liquid chromatography–diode array detector–tandem mass spectrometry (UPLC-DAD-MS) analysis, with final concentrations of 4.728 wt.%, 7.368 wt.% and 2.658 wt.%, respectively. Successful antimicrobial capacity against Escherichia coli and Staphylococcus aureus was obtained for LEO. The results from this work showed the potential of applying a cascading approach based on microwave-assisted processes to valorise lemon wastes, obtaining natural pigments and antimicrobials to be applied in food, cosmetic and polymer industries.