Follow-up after acute myocarditis is important to detect persisting myocardial dysfunction. However, recovery of atrial function has not been evaluated after acute myocarditis so far. Thirty-five patients with strictly defined acute myocarditis underwent cardiovascular magnetic resonance (CMR, 1.5 T) in the acute stage at baseline (BL) and at 3 months follow-up (FU). The study population included 13 patients with biopsy-proven “cardiomyopathy-like” myocarditis (CLM) and 22 patients with “infarct-like” (ILM) clinical presentation. CMR feature tracking (FT) was performed on conventional cine SSFP sequences. Median LA-GLS increased from 33.2 (14.5; 39.2) at BL to 37.0% (25.2; 44.1, P = 0.0018) at FU in the entire study population. Median LA-GLS also increased from 36.7 (26.5; 42.3) at BL to 41.3% (34.5; 44.8, P = 0.0262) at FU in the ILM subgroup and from 11.3 (6.4; 21.1) at BL to 21.4% (14.2; 30.7, P = 0.0186) at FU in the CLM subgroup. Median RA-GLS significantly increased from BL with 30.8 (22.5; 37.0) to FU with 33.7% (26.8; 45.4, P = 0.0027) in the entire study population. Median RA-GLS also significantly increased from 32.7 (25.8; 41.0) at BL to 35.8% (27.7; 48.0, P = 0.0495) at FU in the ILM subgroup and from 22.8 (13.1; 33.9) at BL to 31.0% (26.0; 40.8, P = 0.0266) at FU in the CLM subgroup. Our findings demonstrate recovery of LA and RA function by CMR-FT strain analyses in patients after acute myocarditis independent from clinical presentation. Monitoring of atrial strain could be an important tool for an individual assessment of healing after acute myocarditis.