This paper describes how layers of carbon nanofibers (CNFs) with a controllable wettability can be synthesized by means of thermal catalytic chemical vapor deposition on nickel-based thin films on oxidized silicon supports. In order to achieve well-adhesive CNF-layers with a uniform surface coverage and tunable wettability without the necessity of post-synthesis treatments, a series of synthesis parameters is investigated: the pretreatment atmosphere (hydrogen or oxygen; 2 h, 500 °C), the use of ethylene (C2H4) or an ethylene/hydrogen (C2H4/H2) mixture as hydrocarbon source, and the growth time (in the range 5–60 min). Fast and uniform CNF-growth is found on reduced Ni-based thin films using C2H4/H2 at a synthesis temperature of 635 °C. The CNF-layers on Ni are superhydrophobic or highly hydrophobic for all growth times, but their adhesion to the support is poor for growth times >30 min. In contrast, the adhesion of CNF-layers on Ni/Ta is excellent. Moreover, the wettability of these as-synthesized CNF-layers can be controlled by variation of the growth time: from superhydrophobic (⩽10 min) to hydrophilic (⩾50 min). CNF-layers with such tunable wettability can be easily integrated in flow channels of silicon-based microfluidic systems, thereby offering numerous applications.