In sub-Saharan Africa, soil fertility management must rely on local fertiliser resources since most smallholder farmers do not have access to industrial fertilisers. In Vilankulo, Mozambique, farmers have access to bat guano and biochar, albeit in small amounts, which makes it even more necessary to manage them correctly to maximise crop productivity. This study was carried out with irrigated maize (Zea mays L.) in a haplic Lixisol during the 2017/2018 and 2019 growing seasons. Nine treatments were established consisting of the application of 5 (G5) and 10 (G10) t ha−1 of guano at sowing, 5 (B5) and 10 (B10) t ha−1 of biochar at sowing, 5 [G5(-1)] and 10 [G10(-1)] t ha−1 of guano one month before sowing, 1 and 4 (B1G4) and 2 and 8 (B2G8) t ha−1 of biochar and guano, respectively, at sowing and an unfertilised control (C). Treatments G10 and B2G8 led to the highest maize yields (3.77 and 2.68 t ha−1 in 2018 and 5.05 and 5.17 t ha−1 in 2019, respectively), and were statistically higher than those of the control (1.35 and 1.63 kg ha−1, respectively). Apparent nitrogen recovery from bat guano was close to 100%, showing almost complete mineralisation during the maize growing season, due to its low carbon/nitrogen ratio and very favourable environmental conditions for mineralisation. Due to the fast release of nutrients, bringing forward the application of the organic amendment before sowing is not recommended, since it reduces nutrient use efficiency. Biochar did not significantly influence maize grain yield or contribute significantly to plant nutrition. To take advantage of its potential effect on some soil properties, its use in combination with other materials of greater fertilising value is recommended.