Although toxicogenic moulds have been identified in municipal waste and composting facilities, only a few reports exist on the occurrence of mycotoxins in compost. Those reports mostly concern sewage sludge as a substrate, tested only a limited range of mycotoxins, and did not monitor the production of mycotoxins during the composting process. Therefore, this study aimed to investigate whether mycotoxins are produced during composting of selectively collected kitchen and garden waste. The study was carried out at pilot scale (550 L reactor with passive aeration). Kitchen waste (59.0% w/w), garden leaves (28.2%), and wood chips (12.8%) were used as a substrate, which was sampled every five days to determine its basic physicochemical characteristics (temperature, moisture, size-fraction content, loss on ignition) and respirometric activity (AT4). The substrate and leachate samples were also tested for the content of eight mycotoxins by HPLC-MS/MS. To screen the local compost market, commercial organic-compost samples were analysed for mycotoxin contamination. The substrate was successfully stabilized after 45 days (thermophilic peak of 62.6 °C, 40.4% mass reduction, 26.9% loss of organic matter, increase in the share of particles in the smallest size fraction, AT4 of 9.82 g O2/kg). Although the substrate was colonised by moulds at an early stage, only trace amounts of mycotoxins were detected in a few samples. Similarly, little or no mycotoxins were found in the commercial compost. Our results suggest a low risk of mycotoxin contamination in biowaste compost produced under appropriate technological conditions. Future research should focus on screening compost produced at smaller scales (e.g., in agricultural/residential compost piles) and on identifying factors associated with the risk of mycotoxin contamination in compost.