Land management systems that comprise the principles of conservation agriculture (CA) can lead to soil organic carbon (SOC) gains over time. Nonetheless, how fertilization regimes interfere with their performance in highly weathered soils is still uncertain. This study presents results on SOC storage, crop yield, and soil resilience from a long-term experiment in southern Brazil (Ponta Grossa – Paraná State) 26 years after its establishment in 1989 combining a gradient of soil disturbance through diverse soil management strategies with contrasting fertilization regimes. We hypothesized that preserving soil structure rebuilt over time through no-till system plays a significant role in SOC persistence and the fertilization regime can impact land management performance on soil resilience and crop yield. The experimental design was laid out as a split plot through completely randomized blocks. The main plots comprised the treatments related to soil management systems: 1) conventional plow-based tillage – CT; 2) minimum tillage (Chiselling replacing plowing) – MT; 3) no-till with one chisel plowing every three years – NTch; and 4) continuous no-till system – NTS. The sub-plots comprised full crop fertilization (FCF) for all crops and low crop fertilization (LCF) by suppressing K and P fertilization and maintaining N in broadcast application. SOC stocks significantly improved as the soil disturbance diminished, resulting in higher soil resilience indexes for NTS and NTch. Differences in SOC stocks between the contrasting treatments NTS and CT were higher under low fertilization, resulting in C and N sequestration rates of 1.14 and 0.14 Mg ha−1 year−1 under LCF compared to 0.77 and 0.08 Mg ha−1 yr−1 in FCF at the 0–100 cm layer. Such higher differences were induced by overall higher SOC stocks of CT when under FCF and higher SOC stocks in subsoil depths promoted by NTS when under LCF. High fertilization treatments produced cumulative yields 1.5 times higher for soybeans and 2.5 times higher for corn throughout the 26 years of the experiment. Labile C fractions extracted by hot water (HWEOC) and K-permanganate (POXC) were systematically increased as the disturbance diminished. Gains in labile fractions were promoted in deeper layers in lower disturbance treatments (NTch and NTS). We conclude that combining conservation agriculture principles ultimately defined the potential for SOC sequestration. The high soil resilience under the NTS in this research indicates a considerable potential to reverse the soil degradation and decline of the SOC and labile fractions by conversion to intensive NTS (high and diversified annual C input) associated with absence of soil disturbance.