Abstract Among biofuel production processes using microalgae biomass, biogas generation seems to be the least complex. Nevertheless, its efficiency is hampered due to the hard cell wall. In order to enhance its anaerobic biodegradability, the present investigation evaluated the effect of two pretreatments (low temperature autohydrolysis at 50 °C for 24 and 48 h incubation and alkaline (0.5, 2 and 5% w/w NaOH dosages)) on Chlorella vulgaris and Scenedesmus sp. The autohydrolysis resulted in 16 and 6% chemical oxygen demand (COD) solubilisation for Chlorella and Scenedesmus , respectively. During thermoalkaline pretreatment, COD in soluble phase (CODsol) was increased up to 19% for Chlorella and 17% for Scenedesmus sp. The highest carbohydrates solubilisation corresponded to 2 and 5% w/w NaOH dosage for 48 h at 50 °C for Chlorella (20%) and Scenedesmus (40–43%). When compared to Chlorella , Scenedesmus biomass exhibited higher carbohydrates solubilisation, although methane yield enhancement was low for both substrates. Best case scenario for Scenedesmus sp. (20% increase) was attained with 5% NaOH at 50 °C for 24 h. Despite the lower carbohydrates solubilisation observed for Chlorella , similar methane yields were similar to Scenedesmus sp. The low methane production enhancement was ascribed to the fact that the organic matter solubilised were exopolymers released during pretreatments rather than intracellular material.