•Extraction conditions influence the suppressiveness ability of compost extracts.•Aggressive temperatures promote a higher extraction of phenolic compounds.•Mild temperatures guarantee the preservation of enzymatic activities.•Protocols based on high temperatures reduce the abundance of actinobacteria.•Mesophilic conditions boost extracts’ suppressiveness according to incubation time. The search for new sustainable alternatives for plant disease control has gained interest in the last decades. Compost extracts are nowadays considered a remarkable alternative to agrochemicals due to their biopesticidal properties. However, these properties could be affected by the different variables of extraction protocols and by starting compost. This work focused on the physicochemical and biological characterization of compost extracts obtained from a wide range of composted materials and different extraction protocols (CEP). CEP-1 and CEP-4 involved incubation at 20 °C for 48 h and 14 days, respectively; CEP-2 incubation for 24 h at 40 °C; while CEP-3 were incubated for 12 h at 70 °C. Electrical conductivity, pH, total organic carbon (TOC) and phenolic content were determined as well as the actinobacterial count and enzyme profiles related to plant pathogen suppression. Additionally, the influence of the different materials and protocols on the in vitro growth inhibition of Alternaria alternata and Botrytis cinerea was determined. The starting materials and extraction protocols significantly influenced the physicochemical and biological characteristics of extracts. Treatments based on long incubation times at 20 °C, as well as those based on short incubation times at 40 °C, resulted in extracts with increased suppressive properties. However, extracts derived from CEP-3 protocol were characterized by high phenolic and TOC content, low functional biodiversity, and a more discreet antagonistic capacity. Therefore, the development and optimization of suitable extraction protocols could lead to compost extracts with increased phytoprotective capacities, thus becoming an effective and sustainable alternative to chemical inputs.