Electrolytic manganese residues (EMR) and alkali-activated laterite-based geopolymers were used to prepare slow-release fertilizers (SRFs) and the physicochemical properties and Mn release behavior of EMR-laterite-based SRFs (SRFs-LA) were studied. MnSO₄·H₂O in EMR transforms into CaMnSi₂O₆, MnO₂ and (NH₄)₂Mn(SO₄)₂·6H₂O after SRFs-LA synthesis. Geopolymers can slow Mn release through ion exchange and can physically encapsulate Mn-containing minerals. Mn release from the SRFs-LA system was primarily influenced by a combination of non-Fick diffusion and skeleton erosion. A comparative pot experiment was also conducted between SRFs-LA and SRFs prepared using alkali/acid-activated geopolymers with EMR (SRFs-alGo/SRFs-acGo) to examine the fertilization efficiency of Guizhou white tea seedlings. Compared with Mg(II), Mn(II) not only played a dominant role in the competitive root absorption process from the soil to the interior of seedlings, but also impeded Fe transportation by regulating the expression of citrate transporters. The slow release of Mn from SRFs-alGo and SRFs-LA could benefit tea seedling growth and protein and photosynthetic pigment synthesis, whereas EMR treatments with Mn burst release damaged the antioxidant system owing to the excessive accumulation of reactive oxygen species in leaves. The Mn released from SRFs-acGo may approach the tolerance limit of tea seedlings growth. The order of fertilizer efficiency for young Guizhou white tea seedlings was as follows: SRFs-LA > SRFs-alGo > SRFs-acGo. Moreover, the cost of SRFs-LA prepared using laterite instead of metakaolin as an active silicon–aluminum source could be reduced by approximately $18.7/t.