This paper describes the use of a dynamical simulation model, called Magma, to evaluate the management scenarios of livestock manure in urban and periurban zones of Mahajanga, Madagascar. Three scenarios were tested: Scenario 1, corresponding to the current crop fertilization practices; Scenario 2, trying to maximize the use of livestock wastes on crops; and Scenario 3, testing the relocation of in-town animal farms to a rural area. By simulation, it has been showed that to manage more efficiently manures a better organization of transportation means is required. This may lead to avoid the lack of organic matter during the high season of market gardening. Environmental risk related to non-collected manures and to excess organic and chemical fertilizer application should be thoroughly considered.