Background The study was conducted to determine occurrence and levels of total aflatoxin and zearalenone in concentrate feedstuffs for dairy animals from selected farms in Malawi. Methods A total of 130 concentrate feedstuff samples were collected in paper bags from 113 randomly selected farms in the three agroecological zones (representing high, mid and low (lakeshore) altitudes) from October and December 2019. Each feed sample was ground and analyzed for total aflatoxin and zearalenone using VICAM Fluorometer Method procedures. Results About 85% of samples comprised of corn (maize) bran (CB), 8% for pigeon pea (PP), 2% for dairy mash, 1% for soybean and <1% for sunflower, rice bran (RB) and rice bran mixed with maize bran respectively. 75% of corn bran and 100% of dairy mash and rice bran samples were positive for zearalenone (i.e. above 100 μg/kg) while other concentrates tested negative. Incidences of total aflatoxin were 32%, 67% and 9% in CB, DM and PP bran samples respectively and negligible in other concentrates. Overall, 32% and 23% of feedstuffs had total aflatoxin concentrations above regulatory limits set by Malawi’s neighboring countries (Tanzania and Mozambique) and US respectively whereas only 6% of all the concentrate feedstuffs had zearalenone concentrations above the regulatory limit enforced by EU. Levels of total aflatoxin and zearalenone in CB were not affected by agroecological zones (P=0.17 and P=0.87) respectively. Mean total aflatoxin concentration was 35.4, 28.1 and 38.2 μg/kg in High, Lakeshore and Mid agroecologies respectively whereas zearalenone concentration was 249.7, 226.8 and 243.9 μg/kg respectively. Conclusion To the best of our knowledge, this is the first study to report prevalence of various mycotoxins in dairy concentrate feedstuffs in Malawi. Aflatoxin and zearalenone contamination in dairy concentrates exist but mostly in levels within tolerable limits at least from the limited timeframe of this study. However, presence of total aflatoxin above regulatory limits in 26 - 34% of corn bran, a major concentrate feedstuff, points to the need for deliberate efforts to ensure levels are kept low in dairy animal feeds for both safety of dairy animals and consumers in Malawi.