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 multidimensionality 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 visualise 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 in Mayomyzon, ontogeny in Priscomyzon, and phylogeny in ‘euphaneropoids’ and Palaeospondylus. Our demonstration of empirical multifactorial variation underscores the need for 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.