Sustainable manure management technologies are needed, and combining anaerobic digestion (AD) for energy generation and aerobic composting (AC) to stabilize digestate and remove emerging contaminants (ECs), including veterinary pharmaceuticals and steroid hormones, is promising. This study identified post AD, AC operating conditions that maximized degradation of study ECs, expected to be present in cattle manure digested using treated municipal wastewater as the water source. Study ECs included sulfamethoxazole (SMX), chlortetracycline (CTC), oxytetracycline (OTC), estrone (E1), and naproxen (NPX). Composting conditions were simulated in bench‐scale reactors, with microorganisms from digestate produced in an AD system (25L scale), by varying temperatures, pH, and carbon source compositions (representing food waste/manure co‐digestion with different residence times). Results indicate maximum SMX biodegradation happened at 35°C, pH 7, and with high levels of easily degradable carbon (≥99, 99, 98%), and maximum E1 biodegradation occurred at 35°C, and with low levels of easily degradable carbon (≥97, 99%). Abiotic degradation was responsible for nearly complete removal of tetracyclines under all conditions and for partial degradation of NPX (between 20–48%). Microorganisms originating from the AD system putatively capable of SMX and E1 biodegradation, or of contributing to biodegradation during the AC phase, were identified, including phylotypes previously shown to biodegrade SMX (Brevundimonas and Alcaligenes).This article is protected by copyright. All rights reserved