Habitat fragmentation, the conversion of landscapes into patchy habitats separated by unsuitable environments, is expected to reduce dispersal among patches. However, its effects on dispersal should depend on dispersal syndromes, i.e. how dispersal covaries with phenotypic traits, because these syndromes can drastically alter dispersal and subsequent ecological and evolutionary dynamics. Our comprehension of whether environmental factors such as habitat fragmentation generate and/or modify dispersal syndromes (i.e. conditional dispersal syndromes) is therefore key for biodiversity forecasting. Here we tested whether habitat fragmentation modulates dispersal syndromes by experimentally manipulating matrix harshness, a critical feature of habitat fragmentation, in ciliate microcosms. We found evidence for dispersal syndromes involving multiple traits linked to morphology (elongation and size), movement (velocity and linearity) and demography (growth rate and maximal population density). More importantly, these syndromes were modified by matrix harshness, with increased differences between residents and dispersers in morphology and movement traits, and decreased differences in growth rate as the matrix became increasingly harsh. Our findings thus reveal that habitat fragmentation can mediate the intensity and form of dispersal syndromes, a context-dependence that could have important consequences for ecological and evolutionary dynamics under environmental changes.