In mulch-based cropping systems, soil cover harbours a lot of organisms that may improve soil fertility but may also affect crop health. In the cotton systems of Cameroon, some millipedes (Diplopoda: Julidae) could become important pests by provoking important seedling damages. This study assesses the influence of mulch on the stand and health of cotton seedlings, as well as diagnoses emergence constraints. Two different assays were carried out during the growing season, one with Calopogonium mucunoides (2001) and the other with Brachiaria ruzisiensis (2002), both as cover crop mulches. The two studied factors were (1) presence or absence of mulch and (2) seed protection (insecticide and/or fungicide). Cotton seeding in non tilled soil showed that seedling stand was globally inferior under mulch compared to nude soil. In the supposed absence of soil structure or texture differences, this constraint seemed to come from exacerbated pressure of soil pests, for which mulch provides favourable habitat. With equivalent insecticide protection, seedling stand resulted significantly greater on nude soil, with less visible symptoms of attacks. On the other hand, mulch provided better growth of seedlings, associated with greater aphid infestation but balanced by seeding precocity that permits escape from delayed arrival of aphids. The major risk associated with seedling in mulch-based cotton is soil pests, whose species impact should be assessed to define sustainable control strategy based on the preservation of beneficial soil macrofauna.