Conditional independence is a crucial concept supporting adequate modelling and efficient reasoning in probabilistics. In knowledge representation, the idea of conditional independence has also been introduced for specific formalisms, such as propositional logic and belief revision. In this paper, the notion of conditional independence is studied in the algebraic framework of approximation fixpoint theory. This gives a language-independent account of conditional independence that can be straightforwardly applied to any logic with fixpoint semantics. It is shown how this notion allows to reduce global reasoning to parallel instances of local reasoning, leading to fixed-parameter tractability results. Furthermore, relations to existing notions of conditional independence are discussed and the framework is applied to normal logic programming.