Evolutionary Cell Biology (ECB) has gained increasing attention in the last decades. Here we explore whether ECB is truly inter-disciplinary through the combination of cellular and evolutionary biology to offer evidence-based insights regarding the major questions of cell evolution. Since 2012, ECB asserts to utilize the increasing potential of high-throughput omics data (in silico) with morpho-functional (in situ) information, although challenges remain for a complete integration. For instance, the limited number of model organisms and cultivation techniques available excludes the majority of the extant diversity of cells from the scope of experimental inquiry. At the conceptual level, the simplification of evolutionary processes influenced by cultural views of evolution, such as adaptationism or Scala Naturae, challenges effective interdisciplinary work. Without a profound understanding of evolutionary theory and an integrative view of cell biology, the formulation of questions and experiments properly addressing evolution and diversification of cell complexities can become misleading. In 2009, we advanced the discovery of a nucleolus in the flagellated unicellular eukaryote Giardia lamblia, and studied nucleolus diversity in other lineages via electron microscopy. Since then, studying evolutionary questions at the cellular level became central to our research. We think that new methodological advances are re-shaping and strengthening the ECB research program and opening its door to experimental scientists. For example, the discovery of new archaea and protozoa and subsequent investigations that coupled in situ approaches with in silico approaches has proven that comprehensive morpho-functional information can be obtained that can only be understood through the merging of the cell biological and evolutionary discipline. Motivated by this, we here explore the history, the challenges, and the opportunities of ECB to motivate researchers to join this emergent field of research. We outline elements that contrast the current ECB discipline from previous integrative attempts. We conclude by elucidating the current disciplinary constraints of ECB and propose considerations towards successfully employing ECB to answer questions pertaining to the evolution of cellular complexity.