His research program focuses on two areas: principles underlying multicellular plant development and mechanisms in auxin biology. A general strategy is to (1) use simple models (such as the Arabidopsis embryo) to address complex questions, (2) integrate methodologies from multiple fields (e.g., microscopy, transcriptomics, genetics, biochemistry, modelling) and (3) focus on major, unresolved questions of fundamental origin.

In past years, his team has made seminal discoveries, including the identification of genes and mechanisms controlling root, vascular tissue, ground tissue and stem cell identity in the Arabidopsis embryo. His team has more recently included evolutionary approaches, and adopted Bryophyte model systems that now allow comparative evolutionary studies, and discovery of ancestral system properties.

Weijers is theme chair for Developmental Biology at the graduate school Experimental Plant Sciences, he is secretary general of the International Association for Sexual Plant Reproduction Research and board member of the International Plant Growth Substances Association and the Dutch Society for Developmental Biology. He is an elected member of the Royal Netherlands Academy of Sciences (KNAW; 2021) and EMBO (2020) and founded the Wageningen Young Academy and Science Café Wageningen. He is senior editor at the Plant Cell, was editor in chief of Plant Reproduction, and acts on the editorial advisory board of Science Signaling.