Sustaining productivity of the rice-based cropping systems in the Eastern Indo-Gangetic Plain (EIGP) requires practices to reverse declining soil fertility resulting from excessive tillage and crop residue removal, while decreasing production costs and increasing farm profits. We hypothesize that the adoption of conservation agriculture (CA), involving minimum tillage, crop residue retention and crop rotation, can address most of these challenges. Therefore, the effects of crop establishment methods – strip planting (SP), bed planting (BP) and conventional tillage (CT); and levels of crop residue retention – high residue (HR) and low residue (LR) on individual crop yield, system yield and profitability were evaluated in a split-plot design over three cropping seasons in two field experiments (Alipur and Digram sites) with contrasting crops and soil types in the EIGP. The SP and BP of non-rice crops were rotated with non-puddled rice establishment; CT of non-rice crops was rotated with puddled transplanted rice. In the legume-dominated system (rice-lentil-mung bean), lentil yields were similar in SP and CT, while lower in BP in crop season 1. A positive effect of high residue over low residue was apparent by crop season 2 and persisted in crop season 3. In crop season 3, the lentil yield increased by 18–23% in SP and BP compared to CT. In the cereal-dominated system (rice-wheat-mung bean), significant yield increases of wheat in SP and BP (7–10%) over CT, and of HR (1–3%) over LR, were detected by crop season 3 but not before. Rice yields under CA practices (non-puddled and HR) were comparable with CT (puddled and LR) in both systems. Improved yield of lentil and wheat with CA was correlated with higher soil water content. The net income of SP increased by 25–28% for dry season crops as compared to CT and was equal with CT for rice cropping systems. Conservation agriculture practices provide opportunities for enhancing crop yield and profitability in intensive rice-based systems of the EIGP of Bangladesh.