The adhesion of alginate hydrogels to solid surfaces was probed by atomic force microscopy (AFM) in the sphere/plane geometry. For this purpose a novel approach has been developed for the immobilization of soft colloidal probes onto AFM-cantilevers, which is inspired by techniques originating from cell biology. The aspiration and consecutive manipulation of hydrogel beads by micropipettes allows the entire manipulation sequence to be carried-out in situ. Hence, any alteration of the hydrogel beads upon drying can be excluded. The adhesive behaviour of alginate hydrogels was first evaluated by determining the distribution of pull-off forces on self-assembled monolayers (SAMs) terminating in different functional groups (-CH3, -OH, -NH2, -COOH). It was demonstrated that solvent exclusion plays practically no role in the adhesion process, in clear difference to solid colloidal probes. The adhesion of alginate beads is dominated by chemical interactions rather than solvent exclusion, in particular in the case of amino-terminated SAMs. The data set acquired on the SAMs provided the framework to relate the adhesion of alginate beads on recombinant spider silk protein films to specific functional groups. The preparation of soft colloidal probes and the presented approach in analysing the adhesive behaviour is not limited to alginate hydrogel beads but can be generally applied for probing and understanding the adhesion behaviour of hydrogels on a wide range of substrates, which would be relevant for various applications such as biomedical surface modification or tissue engineering.