Exceptionally preserved fossils of soft-bodied organisms provide unique evidence of evolutionary history, but they are often contentious; different approaches frequently produce radically different reconstructions of taxa and their affinities. Conflict arises due to difficulties in disentangling the three non-independent factors that underlie all morphological variation within and between fossils: ontogeny, taphonomy and phylogeny. Comparative data from extant organisms can be extremely powerful in this context, but is often difficult to apply given the multi-dimensionality of anatomical variation. Here, we present a multivariate ordination method using discrete morphological character data from modern taxa at different ontogenetic and taphonomic stages (semaphoront and ‘semataphonts’). Analysing multiple axes of morphological variation simultaneously allows us to visualize character combinations that are likely to exist in fossil specimens at intersecting stages of growth and decay, and thus constrain interpretation of fossils. Application to early vertebrates finds variation in fossil specimens to be accounted for by all three axes: primarily decay inMayomyzon, ontogeny inPriscomyzonand phylogeny in ‘euphaneropoids’ andPalaeospondylus. Our demonstration of empirical multi-factorial variation underscores the power of multivariate approaches to fossil interpretation, especially non-biomineralized taxa. As such, this conceptual approach provides a new method for resolving enigmatic taxa throughout the fossil record.